Starting phenix.real_space_refine on Thu Mar 5 12:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bh1_12185/03_2026/7bh1_12185_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bh1_12185/03_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_12185/03_2026/7bh1_12185_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bh1_12185/03_2026/7bh1_12185_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bh1_12185/03_2026/7bh1_12185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bh1_12185/03_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-5986/lib/python3.9/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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 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: 3.36, per 1000 atoms: 0.15 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: 2.09 Conformation dependent library (CDL) restraints added in 497.6 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: 0.52 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: 5.24 Time building geometry restraints manager: 2.85 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: 2.090 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: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.710 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 covalent geometry : bond 0.01412 (11014) covalent geometry : angle 1.14826 (14980) hydrogen bonds : bond 0.14015 ( 679) hydrogen bonds : angle 7.05249 ( 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 : 0.553 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: 0.1913 time to fit residues: 37.5065 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 : 0.510 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.150592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097269 restraints weight = 42357.268| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.15 r_work: 0.3161 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11014 Z= 0.158 Angle : 0.638 6.716 14980 Z= 0.340 Chirality : 0.041 0.170 1802 Planarity : 0.005 0.052 1899 Dihedral : 9.501 86.249 1565 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.44 % Allowed : 13.17 % 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: -1.84 (0.20), residues: 1436 helix: 0.04 (0.17), residues: 853 sheet: -2.34 (0.48), residues: 80 loop : -3.28 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 153 TYR 0.034 0.002 TYR A 381 PHE 0.021 0.002 PHE A 327 TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00339 (11014) covalent geometry : angle 0.63800 (14980) hydrogen bonds : bond 0.05248 ( 679) hydrogen bonds : angle 5.44489 ( 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 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.480 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: 0.8954 (tp) cc_final: 0.8744 (tp) REVERT: A 367 GLN cc_start: 0.8878 (mt0) cc_final: 0.8678 (mt0) REVERT: A 445 MET cc_start: 0.9136 (mtm) cc_final: 0.8905 (mtm) REVERT: A 489 MET cc_start: 0.8824 (mtm) cc_final: 0.8576 (mtm) REVERT: B 530 ASP cc_start: 0.8423 (m-30) cc_final: 0.7996 (m-30) REVERT: B 608 MET cc_start: 0.8898 (mtm) cc_final: 0.8610 (mtt) outliers start: 5 outliers final: 4 residues processed: 114 average time/residue: 0.1981 time to fit residues: 33.9459 Evaluate side-chains 109 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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 = 0.3984 r_free = 0.3984 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095977 restraints weight = 42347.132| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.11 r_work: 0.3147 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11014 Z= 0.200 Angle : 0.613 6.432 14980 Z= 0.326 Chirality : 0.040 0.153 1802 Planarity : 0.004 0.053 1899 Dihedral : 8.362 88.881 1565 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.53 % Allowed : 13.62 % Favored : 85.85 % 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: -1.32 (0.21), residues: 1436 helix: 0.49 (0.17), residues: 857 sheet: -2.23 (0.50), residues: 80 loop : -3.13 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.029 0.002 TYR A 381 PHE 0.015 0.001 PHE A 260 TRP 0.007 0.001 TRP C 32 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00455 (11014) covalent geometry : angle 0.61309 (14980) hydrogen bonds : bond 0.04955 ( 679) hydrogen bonds : angle 5.18378 ( 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 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.464 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 310 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (tt) REVERT: A 357 LEU cc_start: 0.8995 (tp) cc_final: 0.8790 (tp) REVERT: A 489 MET cc_start: 0.8914 (mtm) cc_final: 0.8633 (mtm) REVERT: B 608 MET cc_start: 0.8864 (mtm) cc_final: 0.8583 (mtt) REVERT: C 129 ASP cc_start: 0.9043 (t0) cc_final: 0.8366 (t70) outliers start: 6 outliers final: 4 residues processed: 112 average time/residue: 0.1877 time to fit residues: 31.9038 Evaluate side-chains 108 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 116 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4000 r_free = 0.4000 target = 0.150275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097698 restraints weight = 42186.447| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.12 r_work: 0.3170 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11014 Z= 0.159 Angle : 0.569 6.180 14980 Z= 0.298 Chirality : 0.039 0.151 1802 Planarity : 0.004 0.050 1899 Dihedral : 7.687 88.356 1565 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.88 % Allowed : 13.79 % Favored : 85.32 % 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: -0.77 (0.21), residues: 1436 helix: 0.91 (0.17), residues: 859 sheet: -2.07 (0.50), residues: 80 loop : -2.88 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.028 0.001 TYR A 381 PHE 0.015 0.001 PHE A 260 TRP 0.006 0.001 TRP C 32 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00357 (11014) covalent geometry : angle 0.56864 (14980) hydrogen bonds : bond 0.04521 ( 679) hydrogen bonds : angle 4.88003 ( 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 121 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.566 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 225 ILE cc_start: 0.8520 (tp) cc_final: 0.8273 (tp) REVERT: A 310 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8455 (tt) REVERT: A 357 LEU cc_start: 0.9007 (tp) cc_final: 0.8786 (tp) REVERT: A 430 MET cc_start: 0.8078 (mmm) cc_final: 0.7848 (mmm) REVERT: A 489 MET cc_start: 0.8946 (mtm) cc_final: 0.8644 (mtm) REVERT: B 490 PHE cc_start: 0.8147 (p90) cc_final: 0.7707 (p90) REVERT: B 535 MET cc_start: 0.8483 (tpp) cc_final: 0.8057 (tpp) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.1978 time to fit residues: 35.0494 Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 513 GLN 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: 20.0000 chunk 110 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 86 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.150319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097274 restraints weight = 42221.071| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.14 r_work: 0.3221 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11014 Z= 0.173 Angle : 0.570 7.803 14980 Z= 0.298 Chirality : 0.039 0.149 1802 Planarity : 0.004 0.051 1899 Dihedral : 7.515 88.383 1565 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.97 % Allowed : 14.32 % Favored : 84.70 % 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: -0.58 (0.21), residues: 1436 helix: 1.04 (0.17), residues: 862 sheet: -1.94 (0.50), residues: 80 loop : -2.78 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.025 0.001 TYR A 381 PHE 0.012 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 covalent geometry : bond 0.00393 (11014) covalent geometry : angle 0.56962 (14980) hydrogen bonds : bond 0.04491 ( 679) hydrogen bonds : angle 4.82664 ( 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 114 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.554 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 310 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8524 (tt) REVERT: A 357 LEU cc_start: 0.9030 (tp) cc_final: 0.8816 (tp) REVERT: A 466 ASN cc_start: 0.8399 (m110) cc_final: 0.7991 (m110) REVERT: B 203 MET cc_start: 0.7125 (tmm) cc_final: 0.6856 (tpt) REVERT: B 535 MET cc_start: 0.8507 (tpp) cc_final: 0.8101 (tpp) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.2135 time to fit residues: 35.0207 Evaluate side-chains 112 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 347 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.149563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096502 restraints weight = 42713.519| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.14 r_work: 0.3153 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11014 Z= 0.198 Angle : 0.576 6.896 14980 Z= 0.304 Chirality : 0.039 0.147 1802 Planarity : 0.004 0.050 1899 Dihedral : 7.409 86.035 1565 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.97 % Allowed : 15.12 % 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: -0.45 (0.22), residues: 1436 helix: 1.12 (0.17), residues: 860 sheet: -1.77 (0.51), residues: 80 loop : -2.67 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.023 0.001 TYR A 381 PHE 0.018 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 covalent geometry : bond 0.00455 (11014) covalent geometry : angle 0.57626 (14980) hydrogen bonds : bond 0.04520 ( 679) hydrogen bonds : angle 4.79935 ( 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 114 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.633 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 357 LEU cc_start: 0.9022 (tp) cc_final: 0.8803 (tp) REVERT: A 466 ASN cc_start: 0.8505 (m110) cc_final: 0.8076 (m110) REVERT: A 489 MET cc_start: 0.9002 (mtm) cc_final: 0.8655 (mtm) REVERT: B 535 MET cc_start: 0.8447 (tpp) cc_final: 0.8039 (tpp) outliers start: 11 outliers final: 6 residues processed: 109 average time/residue: 0.1974 time to fit residues: 32.9148 Evaluate side-chains 107 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 132 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4006 r_free = 0.4006 target = 0.150616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097521 restraints weight = 42105.246| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.13 r_work: 0.3168 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11014 Z= 0.163 Angle : 0.555 8.229 14980 Z= 0.290 Chirality : 0.039 0.146 1802 Planarity : 0.004 0.050 1899 Dihedral : 6.868 81.408 1563 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.88 % Allowed : 15.47 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.23 (0.22), residues: 1436 helix: 1.27 (0.17), residues: 860 sheet: -1.54 (0.51), residues: 82 loop : -2.55 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.024 0.001 TYR A 381 PHE 0.013 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 covalent geometry : bond 0.00370 (11014) covalent geometry : angle 0.55527 (14980) hydrogen bonds : bond 0.04334 ( 679) hydrogen bonds : angle 4.67065 ( 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 119 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.424 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: A 225 ILE cc_start: 0.8525 (tp) cc_final: 0.8268 (tp) REVERT: A 327 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: A 489 MET cc_start: 0.9014 (mtm) cc_final: 0.8694 (mtm) REVERT: B 203 MET cc_start: 0.7111 (tmm) cc_final: 0.6808 (tpt) REVERT: B 535 MET cc_start: 0.8440 (tpp) cc_final: 0.8064 (tpp) outliers start: 10 outliers final: 7 residues processed: 113 average time/residue: 0.2060 time to fit residues: 35.3956 Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 347 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET 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: 0.7980 chunk 92 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** 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 = 0.4163 r_free = 0.4163 target = 0.164160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109560 restraints weight = 41928.411| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.19 r_work: 0.3416 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2471 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= 0.136 Angle : 0.538 7.610 14980 Z= 0.279 Chirality : 0.038 0.147 1802 Planarity : 0.004 0.049 1899 Dihedral : 6.537 81.800 1563 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.97 % Allowed : 15.65 % Favored : 83.38 % 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: -0.04 (0.22), residues: 1436 helix: 1.40 (0.17), residues: 860 sheet: -1.35 (0.52), residues: 80 loop : -2.46 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 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 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00305 (11014) covalent geometry : angle 0.53839 (14980) hydrogen bonds : bond 0.04162 ( 679) hydrogen bonds : angle 4.54877 ( 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 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.531 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: 0.8954 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: A 389 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 466 ASN cc_start: 0.8275 (m110) cc_final: 0.7927 (m110) REVERT: A 489 MET cc_start: 0.9062 (mtm) cc_final: 0.8721 (mtm) REVERT: B 203 MET cc_start: 0.7139 (tmm) cc_final: 0.6809 (tpt) REVERT: B 535 MET cc_start: 0.8496 (tpp) cc_final: 0.8197 (tpp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.2015 time to fit residues: 33.4547 Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 347 VAL 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 629 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4160 r_free = 0.4160 target = 0.163864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109566 restraints weight = 42126.240| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.19 r_work: 0.3418 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2555 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= 0.142 Angle : 0.536 7.398 14980 Z= 0.278 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.049 1899 Dihedral : 6.358 80.441 1563 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.06 % Allowed : 15.83 % Favored : 83.11 % 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: 0.07 (0.22), residues: 1436 helix: 1.46 (0.17), residues: 860 sheet: -1.34 (0.52), residues: 80 loop : -2.34 (0.26), residues: 496 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 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00321 (11014) covalent geometry : angle 0.53612 (14980) hydrogen bonds : bond 0.04132 ( 679) hydrogen bonds : angle 4.51792 ( 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 116 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.551 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: 0.8954 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: A 389 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8228 (tp) REVERT: A 466 ASN cc_start: 0.8276 (m110) cc_final: 0.7899 (m110) REVERT: A 489 MET cc_start: 0.9098 (mtm) cc_final: 0.8744 (mtm) REVERT: B 203 MET cc_start: 0.7141 (tmm) cc_final: 0.6821 (tpt) REVERT: B 535 MET cc_start: 0.8478 (tpp) cc_final: 0.8192 (tpp) REVERT: B 568 MET cc_start: 0.7907 (ttm) cc_final: 0.7622 (mtp) outliers start: 12 outliers final: 8 residues processed: 110 average time/residue: 0.1946 time to fit residues: 32.8427 Evaluate side-chains 110 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 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: 9.9990 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4012 r_free = 0.4012 target = 0.151267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098203 restraints weight = 42531.432| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.13 r_work: 0.3180 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11014 Z= 0.169 Angle : 0.551 7.384 14980 Z= 0.288 Chirality : 0.039 0.143 1802 Planarity : 0.004 0.048 1899 Dihedral : 6.324 77.232 1563 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.80 % Allowed : 16.00 % Favored : 83.20 % 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: 0.04 (0.22), residues: 1436 helix: 1.41 (0.17), residues: 861 sheet: -1.27 (0.52), residues: 80 loop : -2.35 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.022 0.002 TYR A 381 PHE 0.012 0.001 PHE C 11 TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00386 (11014) covalent geometry : angle 0.55147 (14980) hydrogen bonds : bond 0.04206 ( 679) hydrogen bonds : angle 4.54557 ( 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 111 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.535 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: 0.8893 (OUTLIER) cc_final: 0.8209 (m-10) REVERT: A 389 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 489 MET cc_start: 0.9052 (mtm) cc_final: 0.8727 (mtm) REVERT: B 203 MET cc_start: 0.7124 (tmm) cc_final: 0.6770 (tpt) REVERT: B 568 MET cc_start: 0.7533 (ttm) cc_final: 0.7308 (mtp) REVERT: C 6 PRO cc_start: 0.8426 (Cg_exo) cc_final: 0.8170 (Cg_endo) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.1991 time to fit residues: 31.9908 Evaluate side-chains 111 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.150660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096024 restraints weight = 41455.456| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.40 r_work: 0.3112 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11014 Z= 0.112 Angle : 0.518 7.147 14980 Z= 0.267 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.050 1899 Dihedral : 5.794 62.257 1563 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.80 % Allowed : 16.00 % Favored : 83.20 % 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: 1.64 (0.17), residues: 861 sheet: -1.17 (0.52), residues: 80 loop : -2.19 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.025 0.001 TYR A 381 PHE 0.011 0.001 PHE A 260 TRP 0.006 0.001 TRP C 32 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00246 (11014) covalent geometry : angle 0.51785 (14980) hydrogen bonds : bond 0.03899 ( 679) hydrogen bonds : angle 4.37905 ( 1986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.04 seconds wall clock time: 90 minutes 11.82 seconds (5411.82 seconds total)