Starting phenix.real_space_refine on Wed Feb 12 03:02:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1m_36795/02_2025/8k1m_36795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1m_36795/02_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_36795/02_2025/8k1m_36795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1m_36795/02_2025/8k1m_36795.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1m_36795/02_2025/8k1m_36795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1m_36795/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.84, per 1000 atoms: 0.82 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: 2.19 Conformation dependent library (CDL) restraints added in 919.1 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: 0.63 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: 1.71 Time building geometry restraints manager: 2.47 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.770 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: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.140 ------------------------------------------------------------------------------- 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= 0.468 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 *********************** 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 : 0.724 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: 1.7588 time to fit residues: 204.7907 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 : 0.734 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093748 restraints weight = 9642.170| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.24 r_work: 0.2921 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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= 0.196 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 *********************** 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 : 0.766 Fit side-chains REVERT: B 67 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7558 (ttt90) REVERT: B 135 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7649 (m-30) REVERT: B 287 ARG cc_start: 0.7631 (mtp-110) cc_final: 0.7329 (mtp-110) REVERT: B 296 MET cc_start: 0.8382 (mmt) cc_final: 0.8121 (mmt) REVERT: B 312 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 124 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7756 (ptp-170) REVERT: C 215 GLU cc_start: 0.8434 (tp30) cc_final: 0.6950 (mt-10) REVERT: D 67 ARG cc_start: 0.8346 (mtm180) cc_final: 0.7304 (mtp85) REVERT: D 212 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7920 (mttm) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.5879 time to fit residues: 144.2927 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 : 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 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: 5.9990 chunk 12 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.111787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092211 restraints weight = 9743.352| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.25 r_work: 0.2895 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.003 0.039 7272 Z= 0.220 Angle : 0.570 8.947 9864 Z= 0.285 Chirality : 0.042 0.148 1173 Planarity : 0.004 0.046 1239 Dihedral : 9.835 62.941 1138 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.20 % Allowed : 12.26 % Favored : 84.54 % 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: -1.13 (0.27), residues: 945 helix: 0.63 (0.23), residues: 514 sheet: -1.23 (0.72), residues: 58 loop : -2.73 (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 0.014 0.001 PHE B 191 TYR 0.005 0.001 TYR D 86 ARG 0.003 0.000 ARG B 402 *********************** 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 94 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7582 (m-30) REVERT: B 272 ARG cc_start: 0.6946 (mmp-170) cc_final: 0.6581 (tpp-160) REVERT: B 287 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.7177 (mtp-110) REVERT: B 296 MET cc_start: 0.8310 (mmt) cc_final: 0.7973 (mmt) REVERT: B 312 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7685 (mp) REVERT: B 350 MET cc_start: 0.7757 (mtt) cc_final: 0.7228 (mtm) REVERT: B 360 PHE cc_start: 0.7234 (t80) cc_final: 0.6995 (t80) REVERT: C 13 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7410 (ptp90) REVERT: C 124 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7725 (ptp-170) REVERT: C 180 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6915 (tm-30) REVERT: D 25 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7356 (mm) REVERT: D 67 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7274 (mtp85) REVERT: D 109 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.8024 (mmt) outliers start: 23 outliers final: 7 residues processed: 85 average time/residue: 1.4374 time to fit residues: 128.6387 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 : 0.880 ------------------------------------------------------------------------------- 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: 0.4980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN D 38 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 = 0.3308 r_free = 0.3308 target = 0.113088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093424 restraints weight = 9740.412| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.27 r_work: 0.2914 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7272 Z= 0.167 Angle : 0.522 8.398 9864 Z= 0.262 Chirality : 0.041 0.141 1173 Planarity : 0.004 0.032 1239 Dihedral : 9.346 59.218 1138 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.06 % Allowed : 13.09 % Favored : 83.84 % 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: -0.90 (0.27), residues: 945 helix: 0.82 (0.24), residues: 514 sheet: -1.08 (0.72), residues: 58 loop : -2.64 (0.26), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.012 0.001 PHE B 191 TYR 0.007 0.001 TYR B 432 ARG 0.001 0.000 ARG B 123 *********************** 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 94 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 272 ARG cc_start: 0.6969 (mmp-170) cc_final: 0.6574 (tpp-160) REVERT: B 287 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7229 (mtp-110) REVERT: B 312 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7661 (mp) REVERT: B 350 MET cc_start: 0.7783 (mtt) cc_final: 0.7394 (mtm) REVERT: B 491 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5512 (mm) REVERT: C 13 ARG cc_start: 0.7621 (ptp90) cc_final: 0.7326 (ptp90) REVERT: C 25 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7782 (mm) REVERT: C 180 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6926 (tm-30) REVERT: D 67 ARG cc_start: 0.8289 (mtm180) cc_final: 0.7280 (mtp85) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 1.4560 time to fit residues: 128.5355 Evaluate side-chains 84 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 212 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 0.0470 overall best weight: 0.4482 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094483 restraints weight = 9620.384| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.26 r_work: 0.2944 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2064 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= 0.148 Angle : 0.505 8.286 9864 Z= 0.254 Chirality : 0.040 0.136 1173 Planarity : 0.004 0.048 1239 Dihedral : 8.951 58.889 1138 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.06 % Allowed : 14.48 % 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: -0.69 (0.27), residues: 945 helix: 0.99 (0.24), residues: 515 sheet: -0.92 (0.73), residues: 58 loop : -2.55 (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 0.012 0.001 PHE B 191 TYR 0.004 0.001 TYR D 86 ARG 0.010 0.000 ARG C 124 *********************** 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 92 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 272 ARG cc_start: 0.6963 (mmp-170) cc_final: 0.6549 (tpp-160) REVERT: B 287 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7250 (mtp-110) REVERT: B 296 MET cc_start: 0.8406 (mmt) cc_final: 0.8018 (mmt) REVERT: B 312 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 360 PHE cc_start: 0.7278 (t80) cc_final: 0.7063 (t80) REVERT: B 385 GLN cc_start: 0.7713 (mt0) cc_final: 0.7494 (mt0) REVERT: C 25 LEU cc_start: 0.8015 (mm) cc_final: 0.7785 (mm) REVERT: C 180 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6921 (tm-30) REVERT: D 25 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7331 (mm) REVERT: D 67 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7297 (mtp85) outliers start: 22 outliers final: 10 residues processed: 83 average time/residue: 1.3952 time to fit residues: 121.8463 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 : 0.785 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 79 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.114109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094478 restraints weight = 9641.887| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.26 r_work: 0.2941 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2175 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= 0.154 Angle : 0.495 8.188 9864 Z= 0.250 Chirality : 0.040 0.135 1173 Planarity : 0.004 0.035 1239 Dihedral : 8.690 59.407 1138 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.37 % Allowed : 15.46 % 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: -0.62 (0.27), residues: 945 helix: 1.03 (0.24), residues: 516 sheet: -0.87 (0.74), residues: 58 loop : -2.51 (0.26), residues: 371 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 0.008 0.000 ARG C 124 *********************** 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 86 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: B 272 ARG cc_start: 0.6890 (mmp-170) cc_final: 0.6468 (tpp-160) REVERT: B 287 ARG cc_start: 0.7635 (mtp-110) cc_final: 0.7272 (mtp-110) REVERT: B 296 MET cc_start: 0.8393 (mmt) cc_final: 0.8015 (mmt) REVERT: B 312 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 360 PHE cc_start: 0.7253 (t80) cc_final: 0.6997 (t80) REVERT: B 385 GLN cc_start: 0.7677 (mt0) cc_final: 0.7455 (mt0) REVERT: C 25 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7792 (mm) REVERT: C 180 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6971 (tm-30) REVERT: C 183 GLN cc_start: 0.8322 (pt0) cc_final: 0.7968 (mp10) REVERT: D 25 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7299 (mm) REVERT: D 67 ARG cc_start: 0.8289 (mtm180) cc_final: 0.7272 (mtp85) outliers start: 17 outliers final: 9 residues processed: 78 average time/residue: 1.4924 time to fit residues: 122.1694 Evaluate side-chains 80 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 82 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.113129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093527 restraints weight = 9706.773| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.26 r_work: 0.2927 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7272 Z= 0.176 Angle : 0.506 8.080 9864 Z= 0.255 Chirality : 0.041 0.136 1173 Planarity : 0.004 0.030 1239 Dihedral : 8.551 58.937 1138 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.06 % Allowed : 15.04 % Favored : 81.89 % 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: -0.65 (0.27), residues: 945 helix: 1.00 (0.23), residues: 518 sheet: -0.88 (0.74), residues: 58 loop : -2.54 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 191 TYR 0.005 0.001 TYR D 86 ARG 0.006 0.000 ARG C 124 *********************** 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: 22 poor density : 67 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: B 272 ARG cc_start: 0.7031 (mmp-170) cc_final: 0.6604 (tpp-160) REVERT: B 287 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7333 (mtp-110) REVERT: B 296 MET cc_start: 0.8472 (mmt) cc_final: 0.8093 (mmt) REVERT: B 350 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6796 (mtm) REVERT: B 385 GLN cc_start: 0.7809 (mt0) cc_final: 0.7598 (mt0) REVERT: B 491 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5563 (mm) REVERT: C 13 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7125 (ptp90) REVERT: C 25 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7831 (mm) REVERT: C 180 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7025 (tm-30) REVERT: C 183 GLN cc_start: 0.8343 (pt0) cc_final: 0.8016 (mp10) REVERT: D 25 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7398 (mm) REVERT: D 67 ARG cc_start: 0.8333 (mtm180) cc_final: 0.7339 (mtp85) outliers start: 22 outliers final: 10 residues processed: 80 average time/residue: 1.6752 time to fit residues: 140.4585 Evaluate side-chains 82 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 350 MET 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 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 105 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.113006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093361 restraints weight = 9719.140| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.26 r_work: 0.2925 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7272 Z= 0.183 Angle : 0.507 8.077 9864 Z= 0.255 Chirality : 0.041 0.137 1173 Planarity : 0.004 0.032 1239 Dihedral : 8.450 58.635 1138 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.65 % Allowed : 15.74 % 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: -0.63 (0.27), residues: 945 helix: 1.01 (0.23), residues: 518 sheet: -0.86 (0.74), residues: 58 loop : -2.53 (0.25), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 D 86 ARG 0.005 0.000 ARG C 124 *********************** 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: 19 poor density : 65 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: B 135 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: B 272 ARG cc_start: 0.7006 (mmp-170) cc_final: 0.6580 (tpp-160) REVERT: B 287 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.7322 (mtp-110) REVERT: B 296 MET cc_start: 0.8473 (mmt) cc_final: 0.8081 (mmt) REVERT: B 350 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6934 (mtm) REVERT: B 363 LEU cc_start: 0.7635 (tp) cc_final: 0.7358 (mp) REVERT: B 385 GLN cc_start: 0.7784 (mt0) cc_final: 0.7570 (mt0) REVERT: B 491 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5456 (mm) REVERT: C 13 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7134 (ptp90) REVERT: C 25 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7842 (mm) REVERT: C 72 ASP cc_start: 0.8301 (p0) cc_final: 0.8043 (p0) REVERT: C 76 ASP cc_start: 0.7645 (m-30) cc_final: 0.7429 (m-30) REVERT: C 180 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7014 (tm-30) REVERT: C 183 GLN cc_start: 0.8316 (pt0) cc_final: 0.8011 (mp10) REVERT: D 25 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7424 (mm) REVERT: D 67 ARG cc_start: 0.8339 (mtm180) cc_final: 0.7335 (mtp85) outliers start: 19 outliers final: 10 residues processed: 75 average time/residue: 1.5125 time to fit residues: 119.2045 Evaluate side-chains 80 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 346 ILE Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 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 105 LEU Chi-restraints excluded: chain D residue 212 LYS 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: 0.0000 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.113862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.094200 restraints weight = 9712.008| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.27 r_work: 0.2937 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2357 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= 0.162 Angle : 0.493 8.189 9864 Z= 0.249 Chirality : 0.040 0.134 1173 Planarity : 0.004 0.030 1239 Dihedral : 8.235 59.702 1138 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.65 % Allowed : 15.60 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.27), residues: 945 helix: 1.11 (0.24), residues: 512 sheet: -0.82 (0.74), residues: 58 loop : -2.52 (0.25), 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 0.012 0.001 PHE B 191 TYR 0.005 0.001 TYR D 86 ARG 0.005 0.000 ARG C 124 *********************** 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 82 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 272 ARG cc_start: 0.6996 (mmp-170) cc_final: 0.6565 (tpp-160) REVERT: B 287 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7315 (mtp-110) REVERT: B 296 MET cc_start: 0.8485 (mmt) cc_final: 0.8088 (mmt) REVERT: B 385 GLN cc_start: 0.7785 (mt0) cc_final: 0.7577 (mt0) REVERT: B 491 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5449 (mm) REVERT: C 13 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7138 (ptp90) REVERT: C 25 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7833 (mm) REVERT: C 180 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7012 (tm-30) REVERT: C 183 GLN cc_start: 0.8301 (pt0) cc_final: 0.7988 (mp10) REVERT: D 25 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7437 (mm) REVERT: D 67 ARG cc_start: 0.8335 (mtm180) cc_final: 0.7337 (mtp85) outliers start: 19 outliers final: 11 residues processed: 74 average time/residue: 1.4980 time to fit residues: 116.2904 Evaluate side-chains 78 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU 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 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 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 105 LEU Chi-restraints excluded: chain D residue 212 LYS 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: 0.8980 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095063 restraints weight = 9870.968| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.29 r_work: 0.2950 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2441 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= 0.145 Angle : 0.481 8.125 9864 Z= 0.243 Chirality : 0.040 0.130 1173 Planarity : 0.004 0.030 1239 Dihedral : 7.970 58.116 1138 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.51 % Allowed : 15.46 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.27), residues: 945 helix: 1.16 (0.24), residues: 513 sheet: -0.77 (0.75), residues: 58 loop : -2.45 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.005 0.000 ARG C 124 ********************** 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 84 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 272 ARG cc_start: 0.6930 (mmp-170) cc_final: 0.6495 (tpp-160) REVERT: B 287 ARG cc_start: 0.7627 (mtp-110) cc_final: 0.7305 (mtp-110) REVERT: B 296 MET cc_start: 0.8472 (mmt) cc_final: 0.8087 (mmt) REVERT: B 385 GLN cc_start: 0.7708 (mt0) cc_final: 0.7504 (mt0) REVERT: B 491 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5403 (mm) REVERT: C 13 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7064 (ptp90) REVERT: C 25 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7824 (mm) REVERT: C 72 ASP cc_start: 0.8222 (p0) cc_final: 0.7961 (p0) REVERT: C 76 ASP cc_start: 0.7549 (m-30) cc_final: 0.7333 (m-30) REVERT: C 180 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6981 (tm-30) REVERT: C 183 GLN cc_start: 0.8247 (pt0) cc_final: 0.7957 (mp10) REVERT: D 13 ARG cc_start: 0.7735 (pmt-80) cc_final: 0.7503 (pmt-80) REVERT: D 25 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7426 (mm) REVERT: D 67 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7331 (mtp85) REVERT: D 134 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8412 (ptp90) outliers start: 18 outliers final: 9 residues processed: 75 average time/residue: 1.5501 time to fit residues: 121.7995 Evaluate side-chains 77 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 25 LEU 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.0070 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.115044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.095378 restraints weight = 9588.141| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.26 r_work: 0.2958 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7272 Z= 0.143 Angle : 0.489 8.139 9864 Z= 0.247 Chirality : 0.040 0.129 1173 Planarity : 0.003 0.030 1239 Dihedral : 7.805 55.945 1138 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.09 % Allowed : 16.02 % Favored : 81.89 % 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: -0.42 (0.27), residues: 945 helix: 1.23 (0.24), residues: 513 sheet: -0.68 (0.76), residues: 58 loop : -2.46 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.002 0.001 HIS B 404 PHE 0.012 0.001 PHE B 191 TYR 0.004 0.001 TYR B 489 ARG 0.005 0.000 ARG C 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.09 seconds wall clock time: 88 minutes 26.90 seconds (5306.90 seconds total)