Starting phenix.real_space_refine on Mon Apr 28 06:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1m_36795/04_2025/8k1m_36795.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 23 5.16 5 C 4573 2.51 5 N 1250 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7148 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3847 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 20, 'TRANS': 508} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'L9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 6.49, per 1000 atoms: 0.91 Number of scatterers: 7148 At special positions: 0 Unit cell: (67.24, 101.68, 109.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 3 15.00 O 1299 8.00 N 1250 7.00 C 4573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 868.1 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 56.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.351A pdb=" N ARG D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.023A pdb=" N ALA D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.670A pdb=" N GLN D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 40 through 63 removed outlier: 3.585A pdb=" N TRP B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 48 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 4.079A pdb=" N THR B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.759A pdb=" N ALA B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.237A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 125 removed outlier: 4.940A pdb=" N MET B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.820A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 169 Processing helix chain 'B' and resid 174 through 200 removed outlier: 4.024A pdb=" N VAL B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 228 removed outlier: 3.546A pdb=" N GLY B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.439A pdb=" N CYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.839A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 275 removed outlier: 4.286A pdb=" N LEU B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 258 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.829A pdb=" N ALA B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 removed outlier: 3.833A pdb=" N SER B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 7.145A pdb=" N ASP B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 4.316A pdb=" N THR B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 388 removed outlier: 3.911A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 405 through 436 removed outlier: 6.935A pdb=" N HIS B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 467 removed outlier: 4.142A pdb=" N GLN B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.696A pdb=" N LEU B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 493 Proline residue: B 476 - end of helix removed outlier: 4.903A pdb=" N TRP B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 4.087A pdb=" N ASN B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 522 through 540 removed outlier: 3.508A pdb=" N ILE B 529 " --> pdb=" O TRP B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.389A pdb=" N ARG C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.671A pdb=" N GLN C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 286 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1140 1.29 - 1.42: 1755 1.42 - 1.55: 4332 1.55 - 1.68: 6 1.68 - 1.81: 39 Bond restraints: 7272 Sorted by residual: bond pdb=" CB7 CDL B 602 " pdb=" OB8 CDL B 602 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.04e+01 bond pdb=" CA7 CDL B 602 " pdb=" OA8 CDL B 602 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.10e-02 8.26e+03 3.51e+01 bond pdb=" C ARG C 53 " pdb=" O ARG C 53 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.32e-02 5.74e+03 3.16e+01 bond pdb=" OB2 CDL B 602 " pdb=" PB2 CDL B 602 " ideal model delta sigma weight residual 1.579 1.653 -0.074 1.50e-02 4.44e+03 2.42e+01 bond pdb=" OA2 CDL B 602 " pdb=" PA1 CDL B 602 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.25e+01 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 9415 2.44 - 4.88: 354 4.88 - 7.32: 75 7.32 - 9.75: 17 9.75 - 12.19: 3 Bond angle restraints: 9864 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 112.23 102.32 9.91 1.26e+00 6.30e-01 6.19e+01 angle pdb=" N MET C 109 " pdb=" CA MET C 109 " pdb=" C MET C 109 " ideal model delta sigma weight residual 113.89 101.70 12.19 1.58e+00 4.01e-01 5.95e+01 angle pdb=" C11 CDL B 602 " pdb=" CA5 CDL B 602 " pdb=" OA6 CDL B 602 " ideal model delta sigma weight residual 111.33 119.99 -8.66 1.32e+00 5.72e-01 4.29e+01 angle pdb=" CA GLU B 299 " pdb=" C GLU B 299 " pdb=" N PRO B 300 " ideal model delta sigma weight residual 117.95 122.97 -5.02 7.70e-01 1.69e+00 4.25e+01 angle pdb=" N LEU D 58 " pdb=" CA LEU D 58 " pdb=" C LEU D 58 " ideal model delta sigma weight residual 111.28 118.35 -7.07 1.09e+00 8.42e-01 4.21e+01 ... (remaining 9859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 4053 23.48 - 46.96: 223 46.96 - 70.44: 33 70.44 - 93.92: 5 93.92 - 117.39: 1 Dihedral angle restraints: 4315 sinusoidal: 1674 harmonic: 2641 Sorted by residual: dihedral pdb=" C VAL D 22 " pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta harmonic sigma weight residual -122.00 -136.07 14.07 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C VAL C 22 " pdb=" N VAL C 22 " pdb=" CA VAL C 22 " pdb=" CB VAL C 22 " ideal model delta harmonic sigma weight residual -122.00 -135.78 13.78 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" CA TRP B 458 " pdb=" C TRP B 458 " pdb=" N LEU B 459 " pdb=" CA LEU B 459 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 4312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1017 0.076 - 0.153: 132 0.153 - 0.229: 14 0.229 - 0.306: 6 0.306 - 0.382: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA VAL D 22 " pdb=" N VAL D 22 " pdb=" C VAL D 22 " pdb=" CB VAL D 22 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA VAL C 22 " pdb=" N VAL C 22 " pdb=" C VAL C 22 " pdb=" CB VAL C 22 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ARG D 108 " pdb=" N ARG D 108 " pdb=" C ARG D 108 " pdb=" CB ARG D 108 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1170 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 601 " 0.082 2.00e-02 2.50e+03 8.12e-02 6.60e+01 pdb=" C39 L9Q B 601 " -0.084 2.00e-02 2.50e+03 pdb=" C40 L9Q B 601 " -0.079 2.00e-02 2.50e+03 pdb=" C41 L9Q B 601 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 108 " 0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ARG C 108 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG C 108 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 109 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 103 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ILE D 103 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE D 103 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 104 " -0.027 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2138 2.82 - 3.34: 6495 3.34 - 3.86: 10986 3.86 - 4.38: 13216 4.38 - 4.90: 23314 Nonbonded interactions: 56149 Sorted by model distance: nonbonded pdb=" OH TYR B 33 " pdb=" OD1 ASN B 144 " model vdw 2.303 3.040 nonbonded pdb=" O ALA B 290 " pdb=" OG1 THR C 98 " model vdw 2.310 3.040 nonbonded pdb=" OG SER D 192 " pdb=" OE2 GLU D 197 " model vdw 2.345 3.040 nonbonded pdb=" OG SER C 192 " pdb=" OE2 GLU C 197 " model vdw 2.345 3.040 nonbonded pdb=" O PRO B 472 " pdb=" OG1 THR B 475 " model vdw 2.346 3.040 ... (remaining 56144 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.890 Find NCS groups from input model: 0.120 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.007 0.075 7272 Z= 0.420 Angle : 1.083 12.192 9864 Z= 0.659 Chirality : 0.057 0.382 1173 Planarity : 0.007 0.115 1239 Dihedral : 14.615 117.395 2637 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.42 % Allowed : 1.25 % Favored : 98.33 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 945 helix: -0.06 (0.24), residues: 501 sheet: -1.37 (0.73), residues: 58 loop : -2.83 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 44 HIS 0.005 0.002 HIS D 193 PHE 0.026 0.003 PHE D 19 TYR 0.008 0.001 TYR B 56 ARG 0.014 0.001 ARG B 544 Details of bonding type rmsd hydrogen bonds : bond 0.11579 ( 286) hydrogen bonds : angle 6.04476 ( 858) covalent geometry : bond 0.00684 ( 7272) covalent geometry : angle 1.08324 ( 9864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7362 (mtp-110) REVERT: B 296 MET cc_start: 0.8061 (mmt) cc_final: 0.7836 (mmt) REVERT: C 60 LYS cc_start: 0.8993 (tttp) cc_final: 0.8785 (tttp) REVERT: C 215 GLU cc_start: 0.8091 (tp30) cc_final: 0.7005 (mt-10) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 1.7438 time to fit residues: 203.1800 Evaluate side-chains 73 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS D 153 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093748 restraints weight = 9642.171| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.25 r_work: 0.2936 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7272 Z= 0.127 Angle : 0.599 8.871 9864 Z= 0.302 Chirality : 0.042 0.143 1173 Planarity : 0.004 0.057 1239 Dihedral : 10.782 85.567 1142 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.37 % Allowed : 11.28 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 945 helix: 0.55 (0.24), residues: 502 sheet: -1.37 (0.71), residues: 58 loop : -2.73 (0.25), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 44 HIS 0.006 0.001 HIS B 404 PHE 0.014 0.001 PHE B 191 TYR 0.006 0.001 TYR B 432 ARG 0.004 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 286) hydrogen bonds : angle 3.74180 ( 858) covalent geometry : bond 0.00292 ( 7272) covalent geometry : angle 0.59915 ( 9864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.723 Fit side-chains REVERT: B 67 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7519 (ttt90) REVERT: B 135 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: B 287 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7309 (mtp-110) REVERT: B 296 MET cc_start: 0.8360 (mmt) cc_final: 0.8101 (mmt) REVERT: B 312 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 124 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7696 (ptp-170) REVERT: C 215 GLU cc_start: 0.8397 (tp30) cc_final: 0.6899 (mt-10) REVERT: D 67 ARG cc_start: 0.8308 (mtm180) cc_final: 0.7249 (mtp85) REVERT: D 212 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7865 (mttm) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.5466 time to fit residues: 140.7419 Evaluate side-chains 78 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092660 restraints weight = 9728.314| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.26 r_work: 0.2902 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7272 Z= 0.128 Angle : 0.560 9.013 9864 Z= 0.280 Chirality : 0.042 0.147 1173 Planarity : 0.004 0.043 1239 Dihedral : 9.805 62.933 1138 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.34 % Allowed : 12.40 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.27), residues: 945 helix: 0.67 (0.24), residues: 514 sheet: -1.21 (0.72), residues: 58 loop : -2.72 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.004 0.001 HIS C 83 PHE 0.014 0.001 PHE B 191 TYR 0.005 0.001 TYR D 86 ARG 0.002 0.000 ARG B 402 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 286) hydrogen bonds : angle 3.42414 ( 858) covalent geometry : bond 0.00306 ( 7272) covalent geometry : angle 0.55991 ( 9864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: B 272 ARG cc_start: 0.6950 (mmp-170) cc_final: 0.6582 (tpp-160) REVERT: B 287 ARG cc_start: 0.7589 (mtp-110) cc_final: 0.7173 (mtp-110) REVERT: B 296 MET cc_start: 0.8361 (mmt) cc_final: 0.8015 (mmt) REVERT: B 312 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7692 (mp) REVERT: B 350 MET cc_start: 0.7766 (mtt) cc_final: 0.7263 (mtm) REVERT: B 360 PHE cc_start: 0.7252 (t80) cc_final: 0.7015 (t80) REVERT: C 13 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7403 (ptp90) REVERT: C 124 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: C 180 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6918 (tm-30) REVERT: D 25 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7343 (mm) REVERT: D 67 ARG cc_start: 0.8256 (mtm180) cc_final: 0.7288 (mtp85) REVERT: D 109 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8044 (mmt) outliers start: 24 outliers final: 7 residues processed: 83 average time/residue: 1.5267 time to fit residues: 133.1848 Evaluate side-chains 81 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN C 193 HIS D 38 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092650 restraints weight = 9753.993| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.26 r_work: 0.2901 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7272 Z= 0.123 Angle : 0.534 8.339 9864 Z= 0.269 Chirality : 0.042 0.144 1173 Planarity : 0.004 0.037 1239 Dihedral : 9.347 59.447 1138 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.90 % Allowed : 12.53 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 945 helix: 0.79 (0.24), residues: 514 sheet: -1.12 (0.72), residues: 58 loop : -2.68 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.004 0.001 HIS B 404 PHE 0.013 0.001 PHE B 191 TYR 0.005 0.001 TYR D 86 ARG 0.002 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 286) hydrogen bonds : angle 3.31406 ( 858) covalent geometry : bond 0.00296 ( 7272) covalent geometry : angle 0.53438 ( 9864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: B 272 ARG cc_start: 0.6960 (mmp-170) cc_final: 0.6561 (tpp-160) REVERT: B 287 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7241 (mtp-110) REVERT: B 296 MET cc_start: 0.8377 (mmt) cc_final: 0.8017 (mmt) REVERT: B 312 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7655 (mp) REVERT: B 350 MET cc_start: 0.7812 (mtt) cc_final: 0.7434 (mtm) REVERT: B 360 PHE cc_start: 0.7238 (t80) cc_final: 0.6974 (t80) REVERT: B 491 LEU cc_start: 0.5857 (OUTLIER) cc_final: 0.5544 (mm) REVERT: C 13 ARG cc_start: 0.7630 (ptp90) cc_final: 0.7346 (ptp90) REVERT: C 25 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7788 (mm) REVERT: C 124 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7769 (ptp-110) REVERT: C 180 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6913 (tm-30) REVERT: D 25 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7309 (mm) REVERT: D 67 ARG cc_start: 0.8277 (mtm180) cc_final: 0.7287 (mtp85) REVERT: D 109 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7998 (mmp) outliers start: 28 outliers final: 12 residues processed: 83 average time/residue: 1.4192 time to fit residues: 123.7153 Evaluate side-chains 86 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 12 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS C 183 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094865 restraints weight = 9639.944| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.26 r_work: 0.2937 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7272 Z= 0.092 Angle : 0.495 8.543 9864 Z= 0.250 Chirality : 0.040 0.135 1173 Planarity : 0.004 0.029 1239 Dihedral : 8.883 59.616 1138 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.79 % Allowed : 14.76 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 945 helix: 0.99 (0.24), residues: 515 sheet: -0.95 (0.73), residues: 58 loop : -2.52 (0.26), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.011 0.001 PHE B 191 TYR 0.004 0.001 TYR D 86 ARG 0.002 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 286) hydrogen bonds : angle 3.16400 ( 858) covalent geometry : bond 0.00208 ( 7272) covalent geometry : angle 0.49509 ( 9864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: B 272 ARG cc_start: 0.6949 (mmp-170) cc_final: 0.6533 (tpp-160) REVERT: B 287 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7246 (mtp-110) REVERT: B 312 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 385 GLN cc_start: 0.7707 (mt0) cc_final: 0.7489 (mt0) REVERT: C 25 LEU cc_start: 0.8029 (mm) cc_final: 0.7792 (mm) REVERT: C 180 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6924 (tm-30) REVERT: D 67 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7284 (mtp85) REVERT: D 109 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8030 (mmp) outliers start: 20 outliers final: 8 residues processed: 79 average time/residue: 1.4513 time to fit residues: 120.3564 Evaluate side-chains 80 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094282 restraints weight = 9646.961| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.26 r_work: 0.2940 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7272 Z= 0.100 Angle : 0.496 8.062 9864 Z= 0.251 Chirality : 0.040 0.135 1173 Planarity : 0.004 0.050 1239 Dihedral : 8.672 59.089 1138 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.79 % Allowed : 14.90 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 945 helix: 1.02 (0.24), residues: 518 sheet: -0.85 (0.74), residues: 58 loop : -2.53 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 191 TYR 0.005 0.001 TYR B 489 ARG 0.011 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 286) hydrogen bonds : angle 3.16530 ( 858) covalent geometry : bond 0.00233 ( 7272) covalent geometry : angle 0.49617 ( 9864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: B 272 ARG cc_start: 0.6927 (mmp-170) cc_final: 0.6502 (tpp-160) REVERT: B 287 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7281 (mtp-110) REVERT: B 312 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 360 PHE cc_start: 0.7286 (t80) cc_final: 0.7065 (t80) REVERT: B 385 GLN cc_start: 0.7749 (mt0) cc_final: 0.7533 (mt0) REVERT: C 13 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7045 (ptp90) REVERT: C 25 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 180 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7000 (tm-30) REVERT: C 183 GLN cc_start: 0.8281 (pt0) cc_final: 0.7940 (mp10) REVERT: D 25 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7312 (mm) REVERT: D 67 ARG cc_start: 0.8311 (mtm180) cc_final: 0.7379 (mtp85) outliers start: 20 outliers final: 8 residues processed: 80 average time/residue: 1.4924 time to fit residues: 125.4292 Evaluate side-chains 82 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 82 optimal weight: 0.1980 chunk 81 optimal weight: 0.0770 chunk 88 optimal weight: 0.0870 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 HIS C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097974 restraints weight = 9635.819| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.27 r_work: 0.2995 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7272 Z= 0.080 Angle : 0.459 8.832 9864 Z= 0.233 Chirality : 0.039 0.122 1173 Planarity : 0.003 0.032 1239 Dihedral : 8.074 55.948 1138 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.09 % Allowed : 15.74 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.27), residues: 945 helix: 1.22 (0.24), residues: 518 sheet: -0.64 (0.75), residues: 58 loop : -2.46 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.002 0.001 HIS B 409 PHE 0.011 0.001 PHE B 191 TYR 0.005 0.001 TYR B 432 ARG 0.012 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.02538 ( 286) hydrogen bonds : angle 3.03254 ( 858) covalent geometry : bond 0.00170 ( 7272) covalent geometry : angle 0.45877 ( 9864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.815 Fit side-chains REVERT: B 67 ARG cc_start: 0.7664 (ttt90) cc_final: 0.7309 (ttt90) REVERT: B 93 ASP cc_start: 0.8691 (p0) cc_final: 0.7715 (p0) REVERT: B 135 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: B 272 ARG cc_start: 0.6869 (mmp-170) cc_final: 0.6426 (tpp-160) REVERT: B 287 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7307 (mtp-110) REVERT: B 296 MET cc_start: 0.8375 (mmt) cc_final: 0.7989 (mmt) REVERT: B 363 LEU cc_start: 0.7649 (tp) cc_final: 0.7357 (mp) REVERT: B 491 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5497 (mm) REVERT: C 25 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7812 (mm) REVERT: C 180 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6998 (tm-30) REVERT: C 183 GLN cc_start: 0.8234 (pt0) cc_final: 0.7927 (mp10) REVERT: D 25 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7332 (mm) REVERT: D 67 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7308 (mtp85) outliers start: 15 outliers final: 6 residues processed: 83 average time/residue: 1.3282 time to fit residues: 116.2078 Evaluate side-chains 77 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.094926 restraints weight = 9672.061| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.27 r_work: 0.2947 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7272 Z= 0.107 Angle : 0.495 7.819 9864 Z= 0.248 Chirality : 0.041 0.131 1173 Planarity : 0.004 0.036 1239 Dihedral : 8.103 55.584 1138 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.23 % Allowed : 16.30 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 945 helix: 1.15 (0.24), residues: 520 sheet: -0.70 (0.75), residues: 58 loop : -2.49 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 44 HIS 0.003 0.001 HIS C 153 PHE 0.012 0.001 PHE B 191 TYR 0.004 0.001 TYR B 91 ARG 0.008 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 286) hydrogen bonds : angle 3.10137 ( 858) covalent geometry : bond 0.00255 ( 7272) covalent geometry : angle 0.49486 ( 9864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: B 272 ARG cc_start: 0.6965 (mmp-170) cc_final: 0.6535 (tpp-160) REVERT: B 287 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7346 (mtp-110) REVERT: B 363 LEU cc_start: 0.7686 (tp) cc_final: 0.7393 (mp) REVERT: B 491 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5484 (mm) REVERT: C 25 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7840 (mm) REVERT: C 180 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7050 (tm-30) REVERT: C 183 GLN cc_start: 0.8268 (pt0) cc_final: 0.7982 (mp10) REVERT: D 25 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7388 (mm) REVERT: D 67 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7376 (mtp85) outliers start: 16 outliers final: 8 residues processed: 77 average time/residue: 1.9853 time to fit residues: 160.6032 Evaluate side-chains 75 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.094885 restraints weight = 9708.197| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.27 r_work: 0.2950 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7272 Z= 0.101 Angle : 0.493 8.467 9864 Z= 0.248 Chirality : 0.040 0.131 1173 Planarity : 0.004 0.038 1239 Dihedral : 7.989 55.247 1138 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.95 % Allowed : 16.57 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 945 helix: 1.26 (0.24), residues: 512 sheet: -0.68 (0.76), residues: 58 loop : -2.49 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 191 TYR 0.004 0.001 TYR D 86 ARG 0.008 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 286) hydrogen bonds : angle 3.10297 ( 858) covalent geometry : bond 0.00237 ( 7272) covalent geometry : angle 0.49252 ( 9864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: B 272 ARG cc_start: 0.6884 (mmp-170) cc_final: 0.6449 (tpp-160) REVERT: B 287 ARG cc_start: 0.7649 (mtp-110) cc_final: 0.7320 (mtp-110) REVERT: B 350 MET cc_start: 0.7746 (mmm) cc_final: 0.7190 (mtt) REVERT: B 363 LEU cc_start: 0.7608 (tp) cc_final: 0.7324 (mp) REVERT: B 491 LEU cc_start: 0.5707 (OUTLIER) cc_final: 0.5473 (mm) REVERT: C 25 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7830 (mm) REVERT: C 180 GLU cc_start: 0.7211 (mt-10) cc_final: 0.7003 (tm-30) REVERT: C 183 GLN cc_start: 0.8226 (pt0) cc_final: 0.7930 (mp10) REVERT: D 25 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7412 (mm) REVERT: D 67 ARG cc_start: 0.8322 (mtm180) cc_final: 0.7339 (mtp85) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 1.6842 time to fit residues: 129.9033 Evaluate side-chains 73 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 79 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.096699 restraints weight = 9834.590| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.30 r_work: 0.2978 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7272 Z= 0.085 Angle : 0.469 8.204 9864 Z= 0.238 Chirality : 0.039 0.125 1173 Planarity : 0.004 0.039 1239 Dihedral : 7.685 52.874 1138 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.81 % Allowed : 16.57 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.27), residues: 945 helix: 1.37 (0.24), residues: 512 sheet: -0.61 (0.76), residues: 58 loop : -2.44 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.011 0.001 PHE B 191 TYR 0.003 0.001 TYR B 91 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 286) hydrogen bonds : angle 3.04266 ( 858) covalent geometry : bond 0.00187 ( 7272) covalent geometry : angle 0.46914 ( 9864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.843 Fit side-chains REVERT: B 67 ARG cc_start: 0.7721 (ttt90) cc_final: 0.7462 (ttt90) REVERT: B 272 ARG cc_start: 0.6936 (mmp-170) cc_final: 0.6488 (tpp-160) REVERT: B 287 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7340 (mtp-110) REVERT: B 296 MET cc_start: 0.8406 (mmt) cc_final: 0.8028 (mmt) REVERT: B 350 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7134 (mtt) REVERT: B 363 LEU cc_start: 0.7643 (tp) cc_final: 0.7374 (mp) REVERT: C 25 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 180 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7074 (tm-30) REVERT: C 183 GLN cc_start: 0.8276 (pt0) cc_final: 0.7934 (mp10) REVERT: D 25 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7452 (mm) REVERT: D 67 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7421 (mtp85) REVERT: D 134 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8419 (ptp90) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 1.5098 time to fit residues: 117.2186 Evaluate side-chains 75 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.0970 chunk 72 optimal weight: 0.0030 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.117283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097616 restraints weight = 9554.548| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.26 r_work: 0.2990 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7272 Z= 0.083 Angle : 0.461 8.508 9864 Z= 0.233 Chirality : 0.039 0.123 1173 Planarity : 0.004 0.040 1239 Dihedral : 7.439 52.100 1138 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.95 % Allowed : 16.71 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 945 helix: 1.44 (0.24), residues: 512 sheet: -0.54 (0.77), residues: 58 loop : -2.39 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 404 PHE 0.011 0.001 PHE B 191 TYR 0.004 0.000 TYR B 91 ARG 0.007 0.000 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.02686 ( 286) hydrogen bonds : angle 3.00177 ( 858) covalent geometry : bond 0.00183 ( 7272) covalent geometry : angle 0.46147 ( 9864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5429.02 seconds wall clock time: 94 minutes 59.00 seconds (5699.00 seconds total)