Starting phenix.real_space_refine on Sat Jul 4 16:45:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bh1_12185/07_2026/7bh1_12185.map" } resolution = 3.38 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= 0.002 sd= 0.088 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6977 2.51 5 N 1818 2.21 5 O 1964 1.98 5 H 11139 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21961 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2827 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 13, 'TRANS': 172} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 421 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.73, per 1000 atoms: 0.17 Number of scatterers: 21961 At special positions: 0 Unit cell: (78.66, 114.885, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 61 16.00 P 1 15.00 O 1964 8.00 N 1818 7.00 C 6977 6.00 H 11139 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 681.7 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: 2628 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 64.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 58 through 82 Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.520A pdb=" N LEU A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.656A pdb=" N LEU A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.528A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.717A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.018A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.823A pdb=" N HIS A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.408A 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 305 removed outlier: 4.393A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.128A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 342 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.604A pdb=" N PHE A 354 " --> pdb=" O HIS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.545A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 397 Processing helix chain 'A' and resid 410 through 438 removed outlier: 3.784A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.685A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 508 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix removed outlier: 3.798A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 25 through 30 removed outlier: 6.338A pdb=" N GLN B 28 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 55 Processing helix chain 'B' and resid 61 through 102 removed outlier: 3.822A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 removed outlier: 3.733A pdb=" N MET B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 247 removed outlier: 4.508A 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: 3.523A pdb=" N LEU B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.037A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.604A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 556 through 595 removed outlier: 4.016A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 4.050A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.875A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.627A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 149 removed outlier: 3.530A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'D' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204 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 120 removed outlier: 3.557A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 107 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE B 131 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 153 Processing sheet with id=AA5, first strand: chain 'B' and resid 466 through 470 removed outlier: 3.894A pdb=" N LEU B 304 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 470 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N MET B 548 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 324 removed outlier: 3.567A pdb=" N GLN B 318 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 440 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 445 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR B 429 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.741A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1986 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: 5.32 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11127 1.03 - 1.22: 106 1.22 - 1.42: 4295 1.42 - 1.62: 6513 1.62 - 1.81: 112 Bond restraints: 22153 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.532 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" ND2 ASN B 582 " pdb="HD21 ASN B 582 " ideal model delta sigma weight residual 0.860 0.972 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" ND2 ASN B 582 " pdb="HD22 ASN B 582 " ideal model delta sigma weight residual 0.860 0.966 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C21 9Y0 B 801 " pdb=" O7 9Y0 B 801 " ideal model delta sigma weight residual 1.330 1.417 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 22148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 40042 4.54 - 9.08: 139 9.08 - 13.62: 5 13.62 - 18.16: 0 18.16 - 22.71: 1 Bond angle restraints: 40187 Sorted by residual: angle pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " ideal model delta sigma weight residual 127.64 104.93 22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C12 9Y0 B 801 " pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 127.16 114.64 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O 9Y0 B 801 " pdb=" P 9Y0 B 801 " pdb=" O2 9Y0 B 801 " ideal model delta sigma weight residual 120.70 108.37 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C6 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 111.26 122.17 -10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C2 9Y0 B 801 " pdb=" O3 9Y0 B 801 " pdb=" P 9Y0 B 801 " ideal model delta sigma weight residual 119.47 108.60 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 40182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.35: 9766 27.35 - 54.71: 518 54.71 - 82.06: 86 82.06 - 109.42: 4 109.42 - 136.77: 1 Dihedral angle restraints: 10375 sinusoidal: 5715 harmonic: 4660 Sorted by residual: dihedral pdb=" CA LEU A 36 " pdb=" C LEU A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " pdb=" C6 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 183.38 46.61 136.77 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 10372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1471 0.076 - 0.153: 300 0.153 - 0.229: 27 0.229 - 0.305: 3 0.305 - 0.382: 1 Chirality restraints: 1802 Sorted by residual: chirality pdb=" C1 9Y0 B 801 " pdb=" C 9Y0 B 801 " pdb=" C2 9Y0 B 801 " pdb=" O7 9Y0 B 801 " both_signs ideal model delta sigma weight residual False 2.36 2.74 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILE B 580 " pdb=" CA ILE B 580 " pdb=" CG1 ILE B 580 " pdb=" CG2 ILE B 580 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" C PRO B 34 " pdb=" CB PRO B 34 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1799 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 582 " -0.236 2.00e-02 2.50e+03 2.46e-01 9.06e+02 pdb=" CG ASN B 582 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 582 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN B 582 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN B 582 " 0.352 2.00e-02 2.50e+03 pdb="HD22 ASN B 582 " -0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.039 2.00e-02 2.50e+03 7.11e-02 7.58e+01 pdb=" CG ASN B 624 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " -0.124 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.011 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 B 801 " 0.045 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C13 9Y0 B 801 " -0.053 2.00e-02 2.50e+03 pdb=" C14 9Y0 B 801 " -0.035 2.00e-02 2.50e+03 pdb=" C15 9Y0 B 801 " 0.043 2.00e-02 2.50e+03 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.34: 7384 2.34 - 3.04: 65481 3.04 - 3.74: 82049 3.74 - 4.44: 129580 4.44 - 5.14: 200801 Nonbonded interactions: 485295 Sorted by model distance: nonbonded pdb=" OD1 ASN A 447 " pdb=" H ALA C 88 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP B 335 " pdb="HE21 GLN B 338 " model vdw 1.660 2.450 nonbonded pdb=" HE ARG B 365 " pdb=" OG SER B 369 " model vdw 1.666 2.450 nonbonded pdb="HH11 ARG B 167 " pdb=" O PHE B 173 " model vdw 1.683 2.450 nonbonded pdb=" OD1 ASP B 550 " pdb=" H LEU B 551 " model vdw 1.692 2.450 ... (remaining 485290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.140 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.014 0.199 11014 Z= 0.606 Angle : 1.148 22.705 14980 Z= 0.617 Chirality : 0.060 0.382 1802 Planarity : 0.007 0.075 1899 Dihedral : 14.321 136.773 3937 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.35 % Allowed : 11.32 % Favored : 88.33 % 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: -3.52 (0.18), residues: 1436 helix: -1.56 (0.15), residues: 852 sheet: -3.20 (0.48), residues: 67 loop : -3.44 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 32 TYR 0.046 0.004 TYR A 381 PHE 0.041 0.004 PHE A 260 TRP 0.017 0.003 TRP C 32 HIS 0.008 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.01412 / 0.61 (11014) covalent geometry : angle 1.14826 / 0.62 (14980) hydrogen bonds : bond 0.14015 / 9.45 ( 679) hydrogen bonds : angle 7.05249 / 5.09 ( 1986) *********************** 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 127 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 ASP cc_start: 0.8974 (t0) cc_final: 0.8430 (t70) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.2022 time to fit residues: 39.6626 Evaluate side-chains 98 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.151443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098091 restraints weight = 42277.759| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.15 r_work: 0.3172 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11014 Z= 0.155 Angle : 0.633 7.132 14980 Z= 0.335 Chirality : 0.041 0.174 1802 Planarity : 0.005 0.053 1899 Dihedral : 9.297 85.694 1565 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.53 % Allowed : 13.26 % Favored : 86.21 % 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: -1.73 (0.21), residues: 1436 helix: 0.13 (0.17), residues: 853 sheet: -2.30 (0.49), residues: 80 loop : -3.23 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 TYR 0.036 0.002 TYR A 381 PHE 0.022 0.002 PHE A 260 TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11014) covalent geometry : angle 0.63304 / 0.33 (14980) hydrogen bonds : bond 0.05028 / 3.50 ( 679) hydrogen bonds : angle 5.36688 / 3.91 ( 1986) *********************** 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 123 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.8529 (tp30) cc_final: 0.8299 (tp30) REVERT: A 357 LEU cc_start: 0.8948 (tp) cc_final: 0.8733 (tp) REVERT: A 489 MET cc_start: 0.8743 (mtm) cc_final: 0.8509 (mtm) REVERT: B 490 PHE cc_start: 0.8178 (p90) cc_final: 0.7743 (p90) REVERT: B 530 ASP cc_start: 0.8422 (m-30) cc_final: 0.8007 (m-30) REVERT: B 608 MET cc_start: 0.8916 (mtm) cc_final: 0.8645 (mtt) REVERT: C 129 ASP cc_start: 0.8960 (t0) cc_final: 0.8201 (t70) outliers start: 6 outliers final: 5 residues processed: 121 average time/residue: 0.1999 time to fit residues: 37.4849 Evaluate side-chains 107 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 68 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 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 = 0.4015 r_free = 0.4015 target = 0.151588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098385 restraints weight = 41906.634| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.14 r_work: 0.3180 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11014 Z= 0.143 Angle : 0.573 6.392 14980 Z= 0.301 Chirality : 0.039 0.149 1802 Planarity : 0.004 0.055 1899 Dihedral : 7.882 82.933 1565 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.80 % Allowed : 12.82 % Favored : 86.38 % 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: -1.08 (0.21), residues: 1436 helix: 0.69 (0.17), residues: 862 sheet: -2.71 (0.45), residues: 94 loop : -2.94 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.029 0.001 TYR A 381 PHE 0.015 0.001 PHE A 260 TRP 0.007 0.001 TRP C 32 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11014) covalent geometry : angle 0.57327 / 0.30 (14980) hydrogen bonds : bond 0.04644 / 3.26 ( 679) hydrogen bonds : angle 5.01540 / 3.67 ( 1986) *********************** 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8449 (tt) REVERT: A 357 LEU cc_start: 0.8951 (tp) cc_final: 0.8729 (tp) REVERT: A 367 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8769 (mt0) REVERT: A 489 MET cc_start: 0.8895 (mtm) cc_final: 0.8650 (mtm) REVERT: C 75 MET cc_start: 0.7547 (ptt) cc_final: 0.7199 (pmm) outliers start: 9 outliers final: 4 residues processed: 117 average time/residue: 0.1978 time to fit residues: 35.8481 Evaluate side-chains 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098427 restraints weight = 42290.103| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.15 r_work: 0.3179 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11014 Z= 0.150 Angle : 0.558 6.278 14980 Z= 0.292 Chirality : 0.039 0.149 1802 Planarity : 0.004 0.053 1899 Dihedral : 7.431 79.710 1565 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.97 % Allowed : 13.35 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.21), residues: 1436 helix: 1.03 (0.17), residues: 858 sheet: -2.01 (0.50), residues: 80 loop : -2.75 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.027 0.001 TYR A 381 PHE 0.013 0.001 PHE A 260 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11014) covalent geometry : angle 0.55783 / 0.29 (14980) hydrogen bonds : bond 0.04436 / 3.12 ( 679) hydrogen bonds : angle 4.84777 / 3.54 ( 1986) *********************** 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LEU cc_start: 0.8987 (tp) cc_final: 0.8770 (tp) REVERT: A 367 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8811 (mt0) REVERT: A 430 MET cc_start: 0.8065 (mmm) cc_final: 0.7841 (mmm) REVERT: A 471 PHE cc_start: 0.7495 (m-10) cc_final: 0.7254 (m-80) REVERT: A 489 MET cc_start: 0.8925 (mtm) cc_final: 0.8642 (mtm) REVERT: B 203 MET cc_start: 0.7116 (tmm) cc_final: 0.6683 (tpt) REVERT: B 490 PHE cc_start: 0.8107 (p90) cc_final: 0.7677 (p90) REVERT: B 535 MET cc_start: 0.8506 (tpp) cc_final: 0.8083 (tpp) REVERT: C 75 MET cc_start: 0.7560 (ptt) cc_final: 0.7265 (pmm) REVERT: C 129 ASP cc_start: 0.8995 (t0) cc_final: 0.8396 (t70) outliers start: 11 outliers final: 5 residues processed: 116 average time/residue: 0.1760 time to fit residues: 31.6808 Evaluate side-chains 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 2 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4149 r_free = 0.4149 target = 0.163228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108823 restraints weight = 42133.039| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.17 r_work: 0.3407 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11014 Z= 0.157 Angle : 0.550 6.140 14980 Z= 0.287 Chirality : 0.039 0.149 1802 Planarity : 0.004 0.052 1899 Dihedral : 7.053 76.048 1565 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.06 % Allowed : 13.70 % Favored : 85.23 % 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: -0.33 (0.22), residues: 1436 helix: 1.21 (0.17), residues: 859 sheet: -1.86 (0.50), residues: 80 loop : -2.60 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.025 0.001 TYR A 381 PHE 0.011 0.001 PHE A 260 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (11014) covalent geometry : angle 0.54966 / 0.29 (14980) hydrogen bonds : bond 0.04352 / 3.07 ( 679) hydrogen bonds : angle 4.74054 / 3.45 ( 1986) *********************** 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 120 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8146 (mmm) cc_final: 0.7936 (mmm) REVERT: A 489 MET cc_start: 0.9021 (mtm) cc_final: 0.8744 (mtm) REVERT: B 203 MET cc_start: 0.7149 (tmm) cc_final: 0.6749 (tpt) REVERT: B 535 MET cc_start: 0.8586 (tpp) cc_final: 0.8233 (tpp) REVERT: C 129 ASP cc_start: 0.9059 (t0) cc_final: 0.8510 (t70) outliers start: 12 outliers final: 8 residues processed: 115 average time/residue: 0.1850 time to fit residues: 33.0581 Evaluate side-chains 108 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 0.2980 chunk 128 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4167 r_free = 0.4167 target = 0.165212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110591 restraints weight = 42184.453| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.22 r_work: 0.3429 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11014 Z= 0.123 Angle : 0.526 5.988 14980 Z= 0.273 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.051 1899 Dihedral : 6.605 73.248 1565 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.97 % Allowed : 14.50 % Favored : 84.53 % 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: -0.05 (0.22), residues: 1436 helix: 1.44 (0.17), residues: 858 sheet: -1.69 (0.51), residues: 80 loop : -2.47 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 400 TYR 0.024 0.001 TYR A 381 PHE 0.017 0.001 PHE B 377 TRP 0.005 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11014) covalent geometry : angle 0.52615 / 0.27 (14980) hydrogen bonds : bond 0.04123 / 2.91 ( 679) hydrogen bonds : angle 4.58045 / 3.34 ( 1986) *********************** 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8798 (mt0) REVERT: A 430 MET cc_start: 0.8154 (mmm) cc_final: 0.7945 (mmm) REVERT: A 489 MET cc_start: 0.8986 (mtm) cc_final: 0.8696 (mtm) REVERT: B 203 MET cc_start: 0.7060 (tmm) cc_final: 0.6692 (tpt) REVERT: B 535 MET cc_start: 0.8576 (tpp) cc_final: 0.8235 (tpp) REVERT: C 129 ASP cc_start: 0.9029 (t0) cc_final: 0.8496 (t70) outliers start: 11 outliers final: 6 residues processed: 116 average time/residue: 0.1962 time to fit residues: 35.0100 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4168 r_free = 0.4168 target = 0.164685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110207 restraints weight = 41969.462| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.20 r_work: 0.3422 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11014 Z= 0.143 Angle : 0.534 5.947 14980 Z= 0.278 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.050 1899 Dihedral : 6.439 71.225 1565 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.24 % Allowed : 15.03 % Favored : 83.73 % 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: 0.06 (0.22), residues: 1436 helix: 1.48 (0.17), residues: 858 sheet: -1.45 (0.51), residues: 80 loop : -2.36 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.023 0.001 TYR A 381 PHE 0.012 0.001 PHE B 377 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11014) covalent geometry : angle 0.53370 / 0.28 (14980) hydrogen bonds : bond 0.04133 / 2.92 ( 679) hydrogen bonds : angle 4.55956 / 3.32 ( 1986) *********************** 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 125 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: A 327 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8376 (m-10) REVERT: A 389 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8222 (tp) REVERT: A 430 MET cc_start: 0.8174 (mmm) cc_final: 0.7964 (mmm) REVERT: A 489 MET cc_start: 0.8997 (mtm) cc_final: 0.8701 (mtm) REVERT: B 203 MET cc_start: 0.7080 (tmm) cc_final: 0.6734 (tpt) REVERT: B 535 MET cc_start: 0.8546 (tpp) cc_final: 0.8208 (tpp) REVERT: C 129 ASP cc_start: 0.9052 (t0) cc_final: 0.8504 (t70) outliers start: 14 outliers final: 7 residues processed: 119 average time/residue: 0.2022 time to fit residues: 37.5511 Evaluate side-chains 117 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 27 optimal weight: 2.9990 chunk 114 optimal weight: 0.0270 chunk 92 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4174 r_free = 0.4174 target = 0.165223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110758 restraints weight = 41832.541| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.19 r_work: 0.3427 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11014 Z= 0.134 Angle : 0.525 5.896 14980 Z= 0.273 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.050 1899 Dihedral : 6.256 66.286 1565 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.06 % Allowed : 15.03 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.22), residues: 1436 helix: 1.53 (0.17), residues: 859 sheet: -1.33 (0.52), residues: 80 loop : -2.29 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.023 0.001 TYR A 381 PHE 0.010 0.001 PHE A 260 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11014) covalent geometry : angle 0.52465 / 0.27 (14980) hydrogen bonds : bond 0.04067 / 2.88 ( 679) hydrogen bonds : angle 4.50877 / 3.28 ( 1986) *********************** 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 122 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8371 (m-10) REVERT: A 389 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 430 MET cc_start: 0.8185 (mmm) cc_final: 0.7977 (mmm) REVERT: A 489 MET cc_start: 0.8993 (mtm) cc_final: 0.8713 (mtm) REVERT: B 203 MET cc_start: 0.7072 (tmm) cc_final: 0.6746 (tpt) REVERT: B 535 MET cc_start: 0.8509 (tpp) cc_final: 0.8206 (tpp) REVERT: C 129 ASP cc_start: 0.9046 (t0) cc_final: 0.8493 (t70) outliers start: 12 outliers final: 9 residues processed: 117 average time/residue: 0.2032 time to fit residues: 36.8374 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4180 r_free = 0.4180 target = 0.165782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111157 restraints weight = 41881.256| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.20 r_work: 0.3432 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11014 Z= 0.131 Angle : 0.521 5.862 14980 Z= 0.271 Chirality : 0.038 0.141 1802 Planarity : 0.004 0.050 1899 Dihedral : 6.025 54.239 1565 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.97 % Allowed : 15.30 % Favored : 83.73 % 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: 0.27 (0.22), residues: 1436 helix: 1.58 (0.17), residues: 861 sheet: -1.25 (0.53), residues: 80 loop : -2.20 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.028 0.001 TYR A 381 PHE 0.012 0.001 PHE A 471 TRP 0.006 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11014) covalent geometry : angle 0.52064 / 0.27 (14980) hydrogen bonds : bond 0.04021 / 2.85 ( 679) hydrogen bonds : angle 4.45115 / 3.24 ( 1986) *********************** 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 118 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: A 389 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 489 MET cc_start: 0.9003 (mtm) cc_final: 0.8721 (mtm) REVERT: B 203 MET cc_start: 0.7071 (tmm) cc_final: 0.6755 (tpt) REVERT: B 535 MET cc_start: 0.8484 (tpp) cc_final: 0.8202 (tpp) outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.2052 time to fit residues: 35.7745 Evaluate side-chains 115 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 69 optimal weight: 40.0000 chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.4174 r_free = 0.4174 target = 0.165162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110485 restraints weight = 42166.516| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.22 r_work: 0.3420 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11014 Z= 0.146 Angle : 0.528 5.723 14980 Z= 0.276 Chirality : 0.038 0.142 1802 Planarity : 0.004 0.049 1899 Dihedral : 5.974 56.793 1565 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.06 % Allowed : 15.47 % Favored : 83.47 % 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: 0.29 (0.22), residues: 1436 helix: 1.58 (0.17), residues: 861 sheet: -1.18 (0.52), residues: 80 loop : -2.16 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.024 0.001 TYR A 381 PHE 0.010 0.001 PHE A 260 TRP 0.006 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11014) covalent geometry : angle 0.52836 / 0.28 (14980) hydrogen bonds : bond 0.04044 / 2.87 ( 679) hydrogen bonds : angle 4.45933 / 3.24 ( 1986) ********************** 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 119 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8303 (m-10) REVERT: A 389 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (tp) REVERT: A 489 MET cc_start: 0.9007 (mtm) cc_final: 0.8716 (mtm) REVERT: B 203 MET cc_start: 0.7091 (tmm) cc_final: 0.6767 (tpt) REVERT: B 535 MET cc_start: 0.8375 (tpp) cc_final: 0.8096 (tpp) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.2097 time to fit residues: 36.3718 Evaluate side-chains 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.3929 r_free = 0.3929 target = 0.151844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097269 restraints weight = 41410.671| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.42 r_work: 0.3135 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11014 Z= 0.105 Angle : 0.505 5.687 14980 Z= 0.260 Chirality : 0.037 0.141 1802 Planarity : 0.004 0.050 1899 Dihedral : 5.630 55.365 1565 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.88 % Allowed : 15.56 % Favored : 83.55 % 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: 0.52 (0.22), residues: 1436 helix: 1.75 (0.17), residues: 862 sheet: -1.10 (0.52), residues: 80 loop : -2.03 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.027 0.001 TYR A 381 PHE 0.010 0.001 PHE A 260 TRP 0.005 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11014) covalent geometry : angle 0.50477 / 0.26 (14980) hydrogen bonds : bond 0.03795 / 2.69 ( 679) hydrogen bonds : angle 4.32236 / 3.15 ( 1986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5151.29 seconds wall clock time: 88 minutes 9.32 seconds (5289.32 seconds total)