Starting phenix.real_space_refine on Wed Feb 4 12:37:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrl_14918/02_2026/7zrl_14918.cif" } resolution = 4.0 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= 0.006 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 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6945 2.51 5 N 1817 2.21 5 O 1957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10782 Number of models: 1 Model: "" Number of chains: 5 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: "B" Number of atoms: 5003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5003 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1423 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 13, 'TRANS': 175} 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.24 Number of scatterers: 10782 At special positions: 0 Unit cell: (87.032, 111.32, 164.956, 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 1 19.00 S 61 16.00 P 1 15.00 O 1957 8.00 N 1817 7.00 C 6945 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: 0.73 Conformation dependent library (CDL) restraints added in 538.2 milliseconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 63.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 1 through 33 removed outlier: 3.747A pdb=" N GLY A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.557A pdb=" N GLU A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.589A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.569A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 Processing helix chain 'A' and resid 165 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.989A pdb=" N PHE A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 removed outlier: 3.812A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.384A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.441A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.991A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 369 Proline residue: A 362 - end of helix removed outlier: 4.289A pdb=" N GLY A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.764A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 438 removed outlier: 4.834A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.931A pdb=" N ALA A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.952A pdb=" N MET A 445 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.130A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 Proline residue: A 499 - end of helix removed outlier: 3.563A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 26 through 31 removed outlier: 4.184A pdb=" N TRP B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.510A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 removed outlier: 4.248A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 243 removed outlier: 4.076A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 251 through 263 removed outlier: 4.015A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.574A pdb=" N GLY B 268 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 291 through 298 removed outlier: 4.021A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.848A pdb=" N THR B 311 " --> pdb=" O PHD B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 4.481A pdb=" N ALA B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.904A pdb=" N VAL B 439 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 440 " --> pdb=" O SER B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.244A pdb=" N ARG B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 545 removed outlier: 3.717A pdb=" N LYS B 543 " --> pdb=" O THR B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 591 removed outlier: 3.524A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.724A pdb=" N LEU B 602 " --> pdb=" O TYR B 599 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 607 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 636 removed outlier: 3.982A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE B 632 " --> pdb=" O ILE B 628 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.013A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.151A pdb=" N THR C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.610A 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 removed outlier: 3.715A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 removed outlier: 4.230A pdb=" N GLU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.847A pdb=" N GLN A 202 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.926A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 131 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 166 removed outlier: 7.270A pdb=" N SER B 152 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 287 through 289 removed outlier: 3.528A pdb=" N ASP B 550 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N MET B 535 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 512 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 303 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.609A pdb=" N GLN B 318 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 391 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.961A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 132 659 hydrogen bonds defined for protein. 1929 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: 1.79 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1763 1.31 - 1.44: 2702 1.44 - 1.57: 6405 1.57 - 1.69: 1 1.69 - 1.82: 110 Bond restraints: 10981 Sorted by residual: bond pdb=" OD1 PHD B 307 " pdb=" P PHD B 307 " ideal model delta sigma weight residual 1.816 1.576 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta sigma weight residual 1.459 1.482 -0.022 1.33e-02 5.65e+03 2.84e+00 bond pdb=" CG PHD B 307 " pdb=" OD2 PHD B 307 " ideal model delta sigma weight residual 1.218 1.185 0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" C ILE A 145 " pdb=" O ILE A 145 " ideal model delta sigma weight residual 1.237 1.216 0.021 1.32e-02 5.74e+03 2.52e+00 bond pdb=" C MET B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.51e+00 ... (remaining 10976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14610 2.60 - 5.20: 259 5.20 - 7.80: 61 7.80 - 10.40: 14 10.40 - 13.00: 4 Bond angle restraints: 14948 Sorted by residual: angle pdb=" C VAL A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta sigma weight residual 121.14 111.99 9.15 1.75e+00 3.27e-01 2.74e+01 angle pdb=" CB MET A 384 " pdb=" CG MET A 384 " pdb=" SD MET A 384 " ideal model delta sigma weight residual 112.70 125.70 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" CB MET B 392 " pdb=" CG MET B 392 " pdb=" SD MET B 392 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C LEU C 4 " pdb=" CA LEU C 4 " pdb=" CB LEU C 4 " ideal model delta sigma weight residual 115.89 110.26 5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" C LEU A 178 " pdb=" N VAL A 179 " pdb=" CA VAL A 179 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.72e+01 ... (remaining 14943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5832 17.90 - 35.80: 569 35.80 - 53.70: 108 53.70 - 71.60: 11 71.60 - 89.51: 7 Dihedral angle restraints: 6527 sinusoidal: 2430 harmonic: 4097 Sorted by residual: 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 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA THR A 111 " pdb=" C THR A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA MET B 206 " pdb=" C MET B 206 " pdb=" N VAL B 207 " pdb=" CA VAL B 207 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1573 0.075 - 0.150: 210 0.150 - 0.225: 18 0.225 - 0.300: 1 0.300 - 0.375: 1 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CB THR A 113 " pdb=" CA THR A 113 " pdb=" OG1 THR A 113 " pdb=" CG2 THR A 113 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE B 448 " pdb=" CA ILE B 448 " pdb=" CG1 ILE B 448 " pdb=" CG2 ILE B 448 " 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=" CB VAL C 121 " pdb=" CA VAL C 121 " pdb=" CG1 VAL C 121 " pdb=" CG2 VAL C 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1800 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 37 " 0.020 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE B 37 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE B 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 37 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE B 37 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 37 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 214 " -0.039 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 215 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 62 " 0.007 2.00e-02 2.50e+03 1.62e-02 5.28e+00 pdb=" CG TYR A 62 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 62 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 62 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 62 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 62 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 62 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 62 " -0.001 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 2407 2.79 - 3.37: 12541 3.37 - 3.96: 21009 3.96 - 4.55: 28480 4.55 - 5.14: 42182 Nonbonded interactions: 106619 Sorted by model distance: nonbonded pdb=" OG1 THR A 339 " pdb=" O CYS A 344 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS B 450 " pdb=" O SER B 553 " model vdw 2.266 3.120 nonbonded pdb=" OG SER A 325 " pdb=" O ASN C 131 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" O MET C 75 " model vdw 2.285 3.040 nonbonded pdb=" OE2 GLU C 119 " pdb=" OG1 THR C 133 " model vdw 2.291 3.040 ... (remaining 106614 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.530 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.005 0.240 10981 Z= 0.225 Angle : 0.909 12.997 14948 Z= 0.451 Chirality : 0.051 0.375 1803 Planarity : 0.005 0.060 1897 Dihedral : 14.303 89.506 3895 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -1.26 (0.21), residues: 1436 helix: -0.03 (0.16), residues: 841 sheet: -0.92 (0.56), residues: 91 loop : -2.13 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 50 TYR 0.030 0.002 TYR A 62 PHE 0.057 0.003 PHE B 37 TRP 0.024 0.002 TRP B 31 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00469 (10981) covalent geometry : angle 0.90932 (14948) hydrogen bonds : bond 0.07858 ( 659) hydrogen bonds : angle 5.46792 ( 1929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.402 Fit side-chains REVERT: A 384 MET cc_start: 0.8117 (mmm) cc_final: 0.7584 (mmt) REVERT: A 414 MET cc_start: 0.6959 (tpp) cc_final: 0.6299 (mtp) REVERT: B 360 PHE cc_start: 0.7191 (t80) cc_final: 0.6826 (t80) REVERT: B 402 ARG cc_start: 0.7960 (tpp80) cc_final: 0.7407 (mmp80) REVERT: C 50 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7985 (mmm160) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.0831 time to fit residues: 27.3232 Evaluate side-chains 167 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0670 chunk 55 optimal weight: 2.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085337 restraints weight = 25002.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.086345 restraints weight = 13662.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087617 restraints weight = 9754.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087512 restraints weight = 7455.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088739 restraints weight = 6884.752| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10981 Z= 0.134 Angle : 0.605 8.170 14948 Z= 0.303 Chirality : 0.042 0.142 1803 Planarity : 0.004 0.045 1897 Dihedral : 4.568 31.906 1523 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.24 % Allowed : 11.41 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.32 (0.22), residues: 1436 helix: 0.79 (0.18), residues: 855 sheet: -0.63 (0.58), residues: 80 loop : -1.89 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 50 TYR 0.021 0.001 TYR A 381 PHE 0.026 0.002 PHE B 374 TRP 0.013 0.001 TRP A 115 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00301 (10981) covalent geometry : angle 0.60498 (14948) hydrogen bonds : bond 0.03685 ( 659) hydrogen bonds : angle 4.51480 ( 1929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.385 Fit side-chains REVERT: A 302 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 357 LEU cc_start: 0.8994 (mt) cc_final: 0.8348 (tp) REVERT: A 360 MET cc_start: 0.7883 (tmm) cc_final: 0.7647 (tmm) REVERT: B 69 SER cc_start: 0.7240 (m) cc_final: 0.6890 (p) REVERT: B 383 MET cc_start: 0.6570 (mmm) cc_final: 0.5922 (mtt) REVERT: C 50 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8006 (mmm160) REVERT: C 119 GLU cc_start: 0.8138 (pm20) cc_final: 0.7908 (pm20) REVERT: C 130 ASN cc_start: 0.7846 (t0) cc_final: 0.7602 (t0) REVERT: C 162 TYR cc_start: 0.7353 (m-10) cc_final: 0.7126 (m-10) outliers start: 14 outliers final: 11 residues processed: 196 average time/residue: 0.0934 time to fit residues: 27.0513 Evaluate side-chains 182 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 0.0570 chunk 110 optimal weight: 2.9990 chunk 113 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 17 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086078 restraints weight = 25373.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088196 restraints weight = 13254.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089517 restraints weight = 8318.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090500 restraints weight = 6028.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.091160 restraints weight = 4746.899| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10981 Z= 0.109 Angle : 0.581 13.709 14948 Z= 0.286 Chirality : 0.040 0.221 1803 Planarity : 0.004 0.042 1897 Dihedral : 4.336 29.167 1523 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.41 % Allowed : 14.41 % Favored : 84.17 % 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: 0.11 (0.22), residues: 1436 helix: 1.19 (0.18), residues: 854 sheet: -0.46 (0.59), residues: 80 loop : -1.83 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.022 0.001 TYR A 381 PHE 0.037 0.001 PHE B 360 TRP 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00227 (10981) covalent geometry : angle 0.58111 (14948) hydrogen bonds : bond 0.03407 ( 659) hydrogen bonds : angle 4.33140 ( 1929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.414 Fit side-chains REVERT: A 357 LEU cc_start: 0.8964 (mt) cc_final: 0.8285 (tp) REVERT: A 367 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7713 (mm110) REVERT: A 414 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7403 (tpp) REVERT: A 445 MET cc_start: 0.6775 (mmp) cc_final: 0.6493 (mmp) REVERT: B 69 SER cc_start: 0.7196 (m) cc_final: 0.6845 (p) REVERT: B 383 MET cc_start: 0.6853 (mmm) cc_final: 0.6136 (mtt) REVERT: C 50 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7903 (mmm160) REVERT: C 119 GLU cc_start: 0.8149 (pm20) cc_final: 0.7938 (pm20) outliers start: 16 outliers final: 9 residues processed: 210 average time/residue: 0.0909 time to fit residues: 28.6276 Evaluate side-chains 183 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 11 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN C 131 ASN C 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085118 restraints weight = 25328.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.087069 restraints weight = 13524.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088338 restraints weight = 8574.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089159 restraints weight = 6235.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.089692 restraints weight = 4987.215| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.003 0.034 10981 Z= 0.128 Angle : 0.584 9.750 14948 Z= 0.290 Chirality : 0.041 0.221 1803 Planarity : 0.003 0.040 1897 Dihedral : 4.262 33.480 1523 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.03 % Allowed : 17.68 % Favored : 80.28 % 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: 0.30 (0.23), residues: 1436 helix: 1.36 (0.18), residues: 854 sheet: -0.75 (0.58), residues: 83 loop : -1.70 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 326 TYR 0.020 0.001 TYR A 381 PHE 0.027 0.001 PHE B 360 TRP 0.009 0.001 TRP A 364 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00291 (10981) covalent geometry : angle 0.58368 (14948) hydrogen bonds : bond 0.03468 ( 659) hydrogen bonds : angle 4.28186 ( 1929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8422 (t0) REVERT: A 252 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7998 (t0) REVERT: A 357 LEU cc_start: 0.9000 (mt) cc_final: 0.8341 (tp) REVERT: A 445 MET cc_start: 0.7367 (mmp) cc_final: 0.7073 (mmp) REVERT: B 19 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7853 (tttt) REVERT: B 69 SER cc_start: 0.7292 (m) cc_final: 0.6981 (p) REVERT: B 383 MET cc_start: 0.6536 (mmm) cc_final: 0.6210 (mtt) REVERT: C 50 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.7941 (mmm160) REVERT: C 95 ASP cc_start: 0.8198 (m-30) cc_final: 0.7090 (t0) REVERT: C 96 LYS cc_start: 0.8809 (pttt) cc_final: 0.8593 (pttt) REVERT: C 119 GLU cc_start: 0.8168 (pm20) cc_final: 0.7960 (pm20) outliers start: 23 outliers final: 13 residues processed: 191 average time/residue: 0.0877 time to fit residues: 25.4204 Evaluate side-chains 188 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN C 66 HIS C 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084020 restraints weight = 25184.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085989 restraints weight = 13081.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087386 restraints weight = 8194.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088236 restraints weight = 5865.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088817 restraints weight = 4684.364| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10981 Z= 0.108 Angle : 0.565 9.145 14948 Z= 0.280 Chirality : 0.041 0.222 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.160 32.434 1523 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.30 % Allowed : 18.21 % Favored : 79.49 % 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: 0.49 (0.23), residues: 1436 helix: 1.48 (0.18), residues: 856 sheet: -0.64 (0.58), residues: 83 loop : -1.59 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.021 0.001 TYR A 381 PHE 0.024 0.001 PHE B 360 TRP 0.009 0.001 TRP A 167 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00237 (10981) covalent geometry : angle 0.56520 (14948) hydrogen bonds : bond 0.03303 ( 659) hydrogen bonds : angle 4.20150 ( 1929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 THR cc_start: 0.8895 (t) cc_final: 0.8612 (m) REVERT: A 114 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8401 (t0) REVERT: A 252 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7880 (t0) REVERT: A 410 ASP cc_start: 0.7417 (p0) cc_final: 0.7121 (p0) REVERT: A 414 MET cc_start: 0.7966 (mmt) cc_final: 0.7598 (mmp) REVERT: B 19 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7792 (tttt) REVERT: B 69 SER cc_start: 0.7286 (m) cc_final: 0.6972 (p) REVERT: B 383 MET cc_start: 0.6516 (mmm) cc_final: 0.6291 (mtt) REVERT: B 548 MET cc_start: 0.8915 (mtt) cc_final: 0.8693 (mtp) REVERT: C 50 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.7965 (mmm160) REVERT: C 95 ASP cc_start: 0.8220 (m-30) cc_final: 0.7139 (t0) REVERT: C 141 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 157 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7389 (mp10) outliers start: 26 outliers final: 15 residues processed: 201 average time/residue: 0.0858 time to fit residues: 26.3657 Evaluate side-chains 197 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 11 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 87 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 367 GLN B 408 ASN C 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.083949 restraints weight = 25268.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085913 restraints weight = 13371.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087247 restraints weight = 8464.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.088027 restraints weight = 6105.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088399 restraints weight = 4946.620| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10981 Z= 0.111 Angle : 0.573 9.385 14948 Z= 0.283 Chirality : 0.040 0.213 1803 Planarity : 0.003 0.039 1897 Dihedral : 4.121 32.433 1523 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.12 % Allowed : 19.81 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.23), residues: 1436 helix: 1.51 (0.18), residues: 856 sheet: -0.52 (0.59), residues: 83 loop : -1.56 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.021 0.001 TYR A 381 PHE 0.020 0.001 PHE B 360 TRP 0.008 0.001 TRP A 364 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00248 (10981) covalent geometry : angle 0.57320 (14948) hydrogen bonds : bond 0.03346 ( 659) hydrogen bonds : angle 4.18247 ( 1929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 THR cc_start: 0.8795 (t) cc_final: 0.8479 (m) REVERT: A 114 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8402 (t0) REVERT: A 252 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7899 (t0) REVERT: A 410 ASP cc_start: 0.7310 (p0) cc_final: 0.7061 (p0) REVERT: B 19 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7841 (tttt) REVERT: B 69 SER cc_start: 0.7291 (m) cc_final: 0.6964 (p) REVERT: B 383 MET cc_start: 0.6513 (mmm) cc_final: 0.6252 (mtt) REVERT: C 50 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.7917 (mmm160) REVERT: C 95 ASP cc_start: 0.8223 (m-30) cc_final: 0.7142 (t0) REVERT: C 141 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8689 (mt) REVERT: C 157 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: D 13 PHE cc_start: 0.7803 (m-80) cc_final: 0.7470 (m-80) outliers start: 24 outliers final: 11 residues processed: 197 average time/residue: 0.0801 time to fit residues: 24.4101 Evaluate side-chains 191 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 47 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083820 restraints weight = 25342.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085816 restraints weight = 13449.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087118 restraints weight = 8541.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087942 restraints weight = 6243.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088526 restraints weight = 5038.807| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10981 Z= 0.115 Angle : 0.587 9.683 14948 Z= 0.289 Chirality : 0.041 0.178 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.113 32.725 1523 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.21 % Allowed : 19.54 % Favored : 78.25 % 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: 0.55 (0.23), residues: 1436 helix: 1.48 (0.18), residues: 861 sheet: -0.44 (0.59), residues: 83 loop : -1.53 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.021 0.001 TYR A 381 PHE 0.017 0.001 PHE B 360 TRP 0.007 0.001 TRP A 364 HIS 0.007 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00256 (10981) covalent geometry : angle 0.58654 (14948) hydrogen bonds : bond 0.03374 ( 659) hydrogen bonds : angle 4.17128 ( 1929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8457 (t0) REVERT: A 252 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7863 (t0) REVERT: A 282 MET cc_start: 0.8877 (tmm) cc_final: 0.8460 (tmm) REVERT: A 397 MET cc_start: 0.7967 (mtt) cc_final: 0.7767 (mtm) REVERT: B 19 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7858 (tttt) REVERT: B 69 SER cc_start: 0.7277 (m) cc_final: 0.6963 (p) REVERT: B 383 MET cc_start: 0.6614 (mmm) cc_final: 0.6330 (mtm) REVERT: C 50 ARG cc_start: 0.8378 (mmm-85) cc_final: 0.7842 (mmm160) REVERT: C 95 ASP cc_start: 0.8241 (m-30) cc_final: 0.7179 (t0) REVERT: C 141 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8670 (mt) REVERT: C 157 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: D 13 PHE cc_start: 0.7811 (m-80) cc_final: 0.7482 (m-80) outliers start: 25 outliers final: 14 residues processed: 197 average time/residue: 0.0815 time to fit residues: 24.6051 Evaluate side-chains 192 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.086019 restraints weight = 25052.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087867 restraints weight = 13259.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089146 restraints weight = 8469.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090042 restraints weight = 6123.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090447 restraints weight = 4862.250| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10981 Z= 0.117 Angle : 0.597 9.837 14948 Z= 0.293 Chirality : 0.041 0.215 1803 Planarity : 0.003 0.037 1897 Dihedral : 4.117 33.219 1523 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.21 % Allowed : 20.34 % Favored : 77.45 % 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: 0.57 (0.23), residues: 1436 helix: 1.49 (0.18), residues: 861 sheet: -0.46 (0.59), residues: 83 loop : -1.49 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.021 0.001 TYR A 381 PHE 0.016 0.001 PHE B 360 TRP 0.008 0.001 TRP A 364 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00265 (10981) covalent geometry : angle 0.59669 (14948) hydrogen bonds : bond 0.03383 ( 659) hydrogen bonds : angle 4.17133 ( 1929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8590 (t0) REVERT: A 252 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7772 (t0) REVERT: A 366 MET cc_start: 0.8165 (mmm) cc_final: 0.7829 (tpp) REVERT: B 19 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7827 (tttt) REVERT: B 69 SER cc_start: 0.7235 (m) cc_final: 0.6926 (p) REVERT: B 383 MET cc_start: 0.6598 (mmm) cc_final: 0.6276 (mtm) REVERT: C 50 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7840 (mmm160) REVERT: C 95 ASP cc_start: 0.8174 (m-30) cc_final: 0.7126 (t0) REVERT: C 119 GLU cc_start: 0.7863 (pm20) cc_final: 0.7646 (pt0) REVERT: C 141 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (mt) REVERT: C 157 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7458 (mp10) REVERT: D 13 PHE cc_start: 0.7707 (m-80) cc_final: 0.7428 (m-80) outliers start: 25 outliers final: 14 residues processed: 187 average time/residue: 0.0861 time to fit residues: 24.5583 Evaluate side-chains 190 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081520 restraints weight = 25386.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083402 restraints weight = 13673.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084626 restraints weight = 8815.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.085343 restraints weight = 6506.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.085689 restraints weight = 5370.193| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10981 Z= 0.160 Angle : 0.646 10.418 14948 Z= 0.318 Chirality : 0.042 0.173 1803 Planarity : 0.003 0.036 1897 Dihedral : 4.312 40.749 1523 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 2.21 % Allowed : 21.04 % Favored : 76.75 % 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 (0.23), residues: 1436 helix: 1.37 (0.18), residues: 862 sheet: -0.70 (0.58), residues: 84 loop : -1.49 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.020 0.001 TYR A 381 PHE 0.016 0.001 PHE A 494 TRP 0.011 0.001 TRP A 364 HIS 0.003 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00370 (10981) covalent geometry : angle 0.64597 (14948) hydrogen bonds : bond 0.03735 ( 659) hydrogen bonds : angle 4.25482 ( 1929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8325 (t0) REVERT: A 252 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8073 (t0) REVERT: B 69 SER cc_start: 0.7311 (m) cc_final: 0.7040 (p) REVERT: B 383 MET cc_start: 0.6554 (mmm) cc_final: 0.6178 (mtm) REVERT: C 50 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.7849 (mmm160) REVERT: C 95 ASP cc_start: 0.8179 (m-30) cc_final: 0.7056 (t0) REVERT: C 119 GLU cc_start: 0.8006 (pm20) cc_final: 0.7749 (pt0) REVERT: C 141 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8694 (mt) outliers start: 25 outliers final: 18 residues processed: 183 average time/residue: 0.0835 time to fit residues: 23.3870 Evaluate side-chains 185 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 93 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.085155 restraints weight = 25092.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085941 restraints weight = 14168.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087657 restraints weight = 9859.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.087509 restraints weight = 7087.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087610 restraints weight = 6643.011| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10981 Z= 0.119 Angle : 0.623 11.597 14948 Z= 0.303 Chirality : 0.041 0.172 1803 Planarity : 0.003 0.036 1897 Dihedral : 4.226 37.024 1523 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 2.21 % Allowed : 21.75 % Favored : 76.04 % 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: 0.51 (0.23), residues: 1436 helix: 1.45 (0.18), residues: 860 sheet: -0.85 (0.55), residues: 90 loop : -1.46 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.020 0.001 TYR A 381 PHE 0.026 0.001 PHE A 127 TRP 0.008 0.001 TRP A 364 HIS 0.004 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00265 (10981) covalent geometry : angle 0.62281 (14948) hydrogen bonds : bond 0.03484 ( 659) hydrogen bonds : angle 4.21833 ( 1929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8428 (t0) REVERT: A 252 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 69 SER cc_start: 0.7234 (m) cc_final: 0.7003 (p) REVERT: B 383 MET cc_start: 0.6561 (mmm) cc_final: 0.6203 (mtm) REVERT: C 50 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7880 (mmm160) REVERT: C 95 ASP cc_start: 0.8215 (m-30) cc_final: 0.7192 (t0) REVERT: C 119 GLU cc_start: 0.7950 (pm20) cc_final: 0.7670 (pt0) REVERT: C 141 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8648 (mt) outliers start: 25 outliers final: 20 residues processed: 191 average time/residue: 0.0746 time to fit residues: 21.7258 Evaluate side-chains 192 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain C residue 161 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/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-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7767 > 50: distance: 12 - 13: 3.340 distance: 13 - 14: 11.129 distance: 13 - 16: 7.564 distance: 14 - 15: 6.355 distance: 14 - 21: 5.812 distance: 15 - 174: 8.037 distance: 16 - 17: 5.975 distance: 17 - 18: 3.621 distance: 18 - 20: 3.089 distance: 21 - 22: 9.836 distance: 22 - 23: 10.304 distance: 22 - 25: 6.566 distance: 23 - 26: 3.060 distance: 26 - 27: 9.269 distance: 27 - 28: 4.926 distance: 27 - 30: 13.411 distance: 28 - 29: 13.149 distance: 28 - 32: 13.142 distance: 30 - 31: 5.124 distance: 32 - 33: 10.475 distance: 33 - 34: 8.050 distance: 33 - 36: 17.836 distance: 34 - 35: 8.807 distance: 34 - 41: 14.757 distance: 36 - 37: 10.374 distance: 37 - 38: 15.628 distance: 38 - 39: 16.630 distance: 38 - 40: 17.216 distance: 41 - 42: 17.192 distance: 42 - 43: 4.970 distance: 42 - 45: 13.710 distance: 43 - 44: 8.065 distance: 43 - 52: 17.531 distance: 45 - 46: 17.018 distance: 46 - 47: 9.655 distance: 46 - 48: 20.632 distance: 47 - 49: 12.371 distance: 48 - 50: 9.834 distance: 49 - 51: 21.775 distance: 50 - 51: 30.581 distance: 52 - 53: 16.830 distance: 53 - 54: 20.053 distance: 53 - 56: 8.312 distance: 54 - 55: 27.566 distance: 54 - 60: 10.114 distance: 56 - 57: 15.914 distance: 56 - 58: 10.433 distance: 57 - 59: 19.057 distance: 60 - 61: 12.109 distance: 60 - 66: 15.320 distance: 61 - 62: 26.184 distance: 61 - 64: 5.043 distance: 62 - 63: 17.215 distance: 62 - 67: 21.097 distance: 64 - 65: 11.254 distance: 65 - 66: 11.716 distance: 67 - 68: 19.515 distance: 68 - 69: 25.746 distance: 68 - 71: 40.836 distance: 69 - 70: 26.128 distance: 69 - 72: 25.890 distance: 72 - 73: 33.633 distance: 73 - 74: 17.692 distance: 73 - 76: 39.587 distance: 74 - 75: 4.673 distance: 74 - 81: 8.483 distance: 76 - 77: 25.022 distance: 77 - 78: 12.446 distance: 78 - 79: 24.723 distance: 78 - 80: 12.248 distance: 81 - 82: 16.629 distance: 82 - 83: 11.447 distance: 83 - 84: 10.064 distance: 83 - 85: 23.255