Starting phenix.real_space_refine on Thu Aug 6 02:25:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxh_64583/08_2026/9uxh_64583.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 54 5.49 5 S 28 5.16 5 C 7800 2.51 5 N 2191 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12615 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 570 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "B" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain: "E" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1730 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain: "F" Number of atoms: 5265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5265 Classifications: {'peptide': 653} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 628} Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3138 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1359 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 160} Time building chain proxies: 2.24, per 1000 atoms: 0.18 Number of scatterers: 12615 At special positions: 0 Unit cell: (89.38, 131.2, 180.4, 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 28 16.00 P 54 15.00 O 2542 8.00 N 2191 7.00 C 7800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 489.4 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 6 sheets defined 67.7% alpha, 5.6% beta 18 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'E' and resid 228 through 244 removed outlier: 3.631A pdb=" N SER E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 278 through 317 Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.321A pdb=" N SER E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.915A pdb=" N ILE E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 376 Processing helix chain 'E' and resid 386 through 416 Processing helix chain 'E' and resid 424 through 439 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'F' and resid 39 through 41 No H-bonds generated for 'chain 'F' and resid 39 through 41' Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 150 through 155 Processing helix chain 'F' and resid 161 through 166 removed outlier: 4.235A pdb=" N ALA F 166 " --> pdb=" O GLN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 192 Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 196 through 227 Processing helix chain 'F' and resid 230 through 245 Processing helix chain 'F' and resid 257 through 271 Processing helix chain 'F' and resid 274 through 277 Processing helix chain 'F' and resid 278 through 285 Processing helix chain 'F' and resid 286 through 334 removed outlier: 3.738A pdb=" N ASN F 321 " --> pdb=" O ASN F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 347 Processing helix chain 'F' and resid 356 through 361 Processing helix chain 'F' and resid 361 through 376 removed outlier: 3.882A pdb=" N GLU F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 376 " --> pdb=" O LEU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 416 Processing helix chain 'F' and resid 417 through 420 Processing helix chain 'F' and resid 424 through 442 Processing helix chain 'F' and resid 445 through 469 Processing helix chain 'F' and resid 470 through 491 Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 524 through 528 Processing helix chain 'F' and resid 530 through 552 Processing helix chain 'F' and resid 566 through 570 removed outlier: 3.750A pdb=" N VAL F 569 " --> pdb=" O PRO F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 577 removed outlier: 3.530A pdb=" N HIS F 577 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 591 removed outlier: 3.525A pdb=" N GLN F 591 " --> pdb=" O ALA F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 612 Processing helix chain 'F' and resid 626 through 631 removed outlier: 3.995A pdb=" N LYS F 630 " --> pdb=" O SER F 626 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 626 through 631' Processing helix chain 'F' and resid 649 through 653 Processing helix chain 'C' and resid 3 through 29 removed outlier: 4.333A pdb=" N SER C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA C 8 " --> pdb=" O ASN C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 87 removed outlier: 3.563A pdb=" N TRP C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 115 Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 188 through 209 Processing helix chain 'C' and resid 218 through 246 Processing helix chain 'C' and resid 259 through 268 removed outlier: 3.796A pdb=" N ILE C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 296 removed outlier: 3.813A pdb=" N LEU C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 325 removed outlier: 3.874A pdb=" N TYR C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 378 through 384 removed outlier: 3.564A pdb=" N LYS C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 17 through 37 removed outlier: 3.598A pdb=" N LYS D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.615A pdb=" N LEU D 45 " --> pdb=" O HIS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.853A pdb=" N VAL D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 removed outlier: 3.928A pdb=" N PHE D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 110 removed outlier: 3.847A pdb=" N LEU D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N HIS D 90 " --> pdb=" O PRO D 86 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 94 " --> pdb=" O HIS D 90 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 156 Processing helix chain 'D' and resid 158 through 166 Processing sheet with id=AA1, first strand: chain 'E' and resid 329 through 330 removed outlier: 3.927A pdb=" N LEU E 329 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 382 " --> pdb=" O LEU E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 20 through 23 removed outlier: 5.294A pdb=" N ILE F 5 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS F 75 " --> pdb=" O ILE F 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG F 86 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN F 96 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 159 through 160 removed outlier: 6.206A pdb=" N ASN F 30 " --> pdb=" O VAL F 620 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP F 622 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE F 32 " --> pdb=" O ASP F 622 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N VAL F 29 " --> pdb=" O LEU F 637 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N GLU F 639 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU F 31 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TRP F 641 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR F 33 " --> pdb=" O TRP F 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 505 through 507 Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 52 removed outlier: 7.167A pdb=" N SER C 51 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU C 97 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N THR C 161 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE C 96 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE C 163 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU C 98 " --> pdb=" O ILE C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 113 through 115 708 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3945 1.34 - 1.46: 2920 1.46 - 1.58: 5937 1.58 - 1.70: 107 1.70 - 1.83: 45 Bond restraints: 12954 Sorted by residual: bond pdb=" C3' DG A 27 " pdb=" C2' DG A 27 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG A 14 " pdb=" C2' DG A 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C3' DG B 40 " pdb=" C2' DG B 40 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DC B 42 " pdb=" C2' DC B 42 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.80e+00 bond pdb=" C3' DT B 48 " pdb=" C2' DT B 48 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.55e+00 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 17533 2.56 - 5.12: 183 5.12 - 7.68: 13 7.68 - 10.24: 5 10.24 - 12.80: 3 Bond angle restraints: 17737 Sorted by residual: angle pdb=" C ARG C 224 " pdb=" N LEU C 225 " pdb=" CA LEU C 225 " ideal model delta sigma weight residual 121.14 110.32 10.82 1.75e+00 3.27e-01 3.82e+01 angle pdb=" N LEU C 225 " pdb=" CA LEU C 225 " pdb=" CB LEU C 225 " ideal model delta sigma weight residual 110.40 117.61 -7.21 1.63e+00 3.76e-01 1.96e+01 angle pdb=" N3 DT B 41 " pdb=" C4 DT B 41 " pdb=" O4 DT B 41 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT A 30 " pdb=" C4 DT A 30 " pdb=" O4 DT A 30 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT B 47 " pdb=" C4 DT B 47 " pdb=" O4 DT B 47 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 17732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 6723 16.00 - 32.00: 708 32.00 - 48.01: 253 48.01 - 64.01: 113 64.01 - 80.01: 14 Dihedral angle restraints: 7811 sinusoidal: 3586 harmonic: 4225 Sorted by residual: dihedral pdb=" CA THR C 47 " pdb=" C THR C 47 " pdb=" N GLY C 48 " pdb=" CA GLY C 48 " ideal model delta harmonic sigma weight residual 180.00 133.24 46.76 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" CA ILE C 215 " pdb=" C ILE C 215 " pdb=" N VAL C 216 " pdb=" CA VAL C 216 " ideal model delta harmonic sigma weight residual 180.00 141.64 38.36 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA ASP C 41 " pdb=" C ASP C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta harmonic sigma weight residual -180.00 -147.87 -32.13 0 5.00e+00 4.00e-02 4.13e+01 ... (remaining 7808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1941 0.101 - 0.201: 60 0.201 - 0.302: 2 0.302 - 0.402: 0 0.402 - 0.503: 1 Chirality restraints: 2004 Sorted by residual: chirality pdb=" CG LEU C 225 " pdb=" CB LEU C 225 " pdb=" CD1 LEU C 225 " pdb=" CD2 LEU C 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA PHE C 221 " pdb=" N PHE C 221 " pdb=" C PHE C 221 " pdb=" CB PHE C 221 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU C 26 " pdb=" CB LEU C 26 " pdb=" CD1 LEU C 26 " pdb=" CD2 LEU C 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2001 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 32 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C SER C 32 " -0.050 2.00e-02 2.50e+03 pdb=" O SER C 32 " 0.019 2.00e-02 2.50e+03 pdb=" N SER C 33 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 221 " -0.025 2.00e-02 2.50e+03 1.82e-02 5.77e+00 pdb=" CG PHE C 221 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 221 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 221 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 221 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE C 221 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 221 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 221 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C PHE C 221 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE C 221 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 222 " 0.011 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 286 2.68 - 3.24: 12693 3.24 - 3.79: 21520 3.79 - 4.35: 28159 4.35 - 4.90: 44599 Nonbonded interactions: 107257 Sorted by model distance: nonbonded pdb=" OH TYR F 275 " pdb=" O TYR F 423 " model vdw 2.125 3.040 nonbonded pdb=" O THR C 47 " pdb=" NE ARG C 217 " model vdw 2.166 3.120 nonbonded pdb=" OG1 THR E 322 " pdb=" OD2 ASP E 325 " model vdw 2.182 3.040 nonbonded pdb=" O ASP C 90 " pdb=" OG1 THR C 94 " model vdw 2.191 3.040 nonbonded pdb=" NZ LYS F 207 " pdb=" OE2 GLU F 211 " model vdw 2.193 3.120 ... (remaining 107252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.220 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.045 12954 Z= 0.261 Angle : 0.665 12.797 17737 Z= 0.414 Chirality : 0.044 0.503 2004 Planarity : 0.004 0.047 2080 Dihedral : 16.233 80.012 5059 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 0.39 % Allowed : 0.78 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1421 helix: 1.90 (0.18), residues: 840 sheet: 0.42 (0.57), residues: 88 loop : 0.29 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 44 TYR 0.017 0.001 TYR D 32 PHE 0.035 0.002 PHE C 221 TRP 0.026 0.001 TRP F 534 HIS 0.004 0.001 HIS F 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.26 (12954) covalent geometry : angle 0.66524 / 0.41 (17737) hydrogen bonds : bond 0.14049 / 15.60 ( 751) hydrogen bonds : angle 5.73486 / 6.35 ( 2162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 397 LEU cc_start: 0.8527 (tp) cc_final: 0.8282 (tp) REVERT: E 424 ASP cc_start: 0.8726 (p0) cc_final: 0.8376 (p0) REVERT: F 203 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7893 (mt0) REVERT: F 218 ARG cc_start: 0.7425 (ttt90) cc_final: 0.6411 (ptm160) REVERT: F 230 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.6054 (m-90) REVERT: F 404 MET cc_start: 0.8677 (mmm) cc_final: 0.8455 (tpp) REVERT: F 454 GLU cc_start: 0.8488 (tt0) cc_final: 0.8240 (tt0) REVERT: C 171 HIS cc_start: 0.8641 (t-90) cc_final: 0.8226 (t-90) REVERT: C 211 ARG cc_start: 0.8750 (mpp80) cc_final: 0.8521 (mpp80) REVERT: D 1 MET cc_start: 0.5215 (ppp) cc_final: 0.4449 (tmm) REVERT: D 116 ASP cc_start: 0.7953 (t0) cc_final: 0.7561 (t0) REVERT: D 161 ASP cc_start: 0.8838 (m-30) cc_final: 0.8592 (m-30) outliers start: 5 outliers final: 1 residues processed: 215 average time/residue: 0.1047 time to fit residues: 31.8856 Evaluate side-chains 121 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 230 TRP Chi-restraints excluded: chain C residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 410 GLN F 312 ASN F 343 GLN F 347 ASN ** F 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.117411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.083906 restraints weight = 36490.863| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 4.00 r_work: 0.3419 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12954 Z= 0.200 Angle : 0.692 8.483 17737 Z= 0.370 Chirality : 0.045 0.253 2004 Planarity : 0.004 0.047 2080 Dihedral : 18.127 66.550 2162 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.09 % Allowed : 8.39 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1421 helix: 1.84 (0.17), residues: 844 sheet: -0.17 (0.52), residues: 95 loop : 0.35 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 415 TYR 0.013 0.001 TYR C 164 PHE 0.033 0.002 PHE C 241 TRP 0.021 0.002 TRP F 526 HIS 0.007 0.001 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (12954) covalent geometry : angle 0.69244 / 0.37 (17737) hydrogen bonds : bond 0.05228 / 5.77 ( 751) hydrogen bonds : angle 4.70357 / 5.62 ( 2162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8323 (m-80) cc_final: 0.7996 (m-80) REVERT: E 424 ASP cc_start: 0.8504 (p0) cc_final: 0.8252 (p0) REVERT: F 203 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8079 (mt0) REVERT: F 404 MET cc_start: 0.9027 (mmm) cc_final: 0.8690 (mmt) REVERT: F 454 GLU cc_start: 0.8419 (tt0) cc_final: 0.8213 (tt0) REVERT: F 473 GLU cc_start: 0.8860 (tp30) cc_final: 0.8509 (tp30) REVERT: C 28 GLU cc_start: 0.8705 (mp0) cc_final: 0.8355 (mm-30) REVERT: C 171 HIS cc_start: 0.8889 (t-90) cc_final: 0.8459 (t-90) REVERT: C 220 ASP cc_start: 0.9049 (t70) cc_final: 0.8824 (p0) REVERT: D 116 ASP cc_start: 0.8437 (t0) cc_final: 0.8084 (t0) REVERT: D 161 ASP cc_start: 0.9038 (m-30) cc_final: 0.8803 (m-30) outliers start: 14 outliers final: 8 residues processed: 130 average time/residue: 0.0926 time to fit residues: 18.4125 Evaluate side-chains 111 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 291 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 19 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.119954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.087159 restraints weight = 36844.079| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.97 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12954 Z= 0.155 Angle : 0.613 9.765 17737 Z= 0.327 Chirality : 0.042 0.326 2004 Planarity : 0.004 0.049 2080 Dihedral : 18.203 63.411 2158 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.79 % Allowed : 10.25 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.23), residues: 1421 helix: 1.95 (0.17), residues: 850 sheet: -0.37 (0.52), residues: 93 loop : 0.39 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 152 TYR 0.014 0.001 TYR D 32 PHE 0.017 0.002 PHE C 99 TRP 0.024 0.001 TRP F 230 HIS 0.009 0.001 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (12954) covalent geometry : angle 0.61321 / 0.33 (17737) hydrogen bonds : bond 0.04604 / 4.98 ( 751) hydrogen bonds : angle 4.48930 / 5.34 ( 2162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 287 GLU cc_start: 0.8781 (pt0) cc_final: 0.8445 (pt0) REVERT: E 404 MET cc_start: 0.7962 (mmm) cc_final: 0.7692 (tpp) REVERT: E 424 ASP cc_start: 0.8464 (p0) cc_final: 0.8153 (p0) REVERT: F 203 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7836 (mt0) REVERT: F 404 MET cc_start: 0.8816 (mmm) cc_final: 0.8446 (mmt) REVERT: F 473 GLU cc_start: 0.8728 (tp30) cc_final: 0.8319 (tp30) REVERT: C 171 HIS cc_start: 0.8824 (t-90) cc_final: 0.8388 (t-90) REVERT: C 209 GLU cc_start: 0.7919 (pm20) cc_final: 0.7650 (pm20) REVERT: C 220 ASP cc_start: 0.8898 (t70) cc_final: 0.8683 (p0) REVERT: D 161 ASP cc_start: 0.9026 (m-30) cc_final: 0.8641 (m-30) outliers start: 23 outliers final: 10 residues processed: 131 average time/residue: 0.0811 time to fit residues: 16.5422 Evaluate side-chains 110 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 291 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 45 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 0.0060 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.118663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.085992 restraints weight = 36611.492| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.92 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12954 Z= 0.160 Angle : 0.594 9.159 17737 Z= 0.318 Chirality : 0.042 0.265 2004 Planarity : 0.004 0.050 2080 Dihedral : 18.207 62.402 2158 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.63 % Allowed : 11.49 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.23), residues: 1421 helix: 2.01 (0.18), residues: 842 sheet: -0.52 (0.54), residues: 83 loop : 0.36 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 472 TYR 0.014 0.001 TYR D 32 PHE 0.015 0.001 PHE C 53 TRP 0.020 0.002 TRP C 199 HIS 0.006 0.001 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (12954) covalent geometry : angle 0.59385 / 0.32 (17737) hydrogen bonds : bond 0.04357 / 4.72 ( 751) hydrogen bonds : angle 4.36630 / 5.21 ( 2162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8618 (m-80) cc_final: 0.8259 (m-80) REVERT: E 404 MET cc_start: 0.8125 (mmm) cc_final: 0.7872 (tpp) REVERT: E 424 ASP cc_start: 0.8444 (p0) cc_final: 0.8183 (p0) REVERT: F 203 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7810 (mt0) REVERT: F 442 MET cc_start: 0.6232 (tmm) cc_final: 0.5050 (ttt) REVERT: F 473 GLU cc_start: 0.8777 (tp30) cc_final: 0.8365 (tp30) REVERT: F 488 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8740 (tp) REVERT: C 171 HIS cc_start: 0.8812 (t-90) cc_final: 0.8413 (t-90) REVERT: C 276 GLU cc_start: 0.8629 (tp30) cc_final: 0.7788 (mm-30) REVERT: D 161 ASP cc_start: 0.9036 (m-30) cc_final: 0.8669 (m-30) outliers start: 21 outliers final: 13 residues processed: 124 average time/residue: 0.0913 time to fit residues: 17.5337 Evaluate side-chains 114 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 112 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.118787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.085984 restraints weight = 36618.099| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.91 r_work: 0.3410 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12954 Z= 0.149 Angle : 0.576 11.901 17737 Z= 0.309 Chirality : 0.041 0.229 2004 Planarity : 0.004 0.050 2080 Dihedral : 18.175 62.136 2158 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 2.02 % Allowed : 11.49 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1421 helix: 2.06 (0.17), residues: 850 sheet: -0.62 (0.54), residues: 83 loop : 0.24 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 152 TYR 0.014 0.001 TYR D 32 PHE 0.011 0.001 PHE C 53 TRP 0.013 0.001 TRP F 230 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12954) covalent geometry : angle 0.57613 / 0.31 (17737) hydrogen bonds : bond 0.04247 / 4.61 ( 751) hydrogen bonds : angle 4.30214 / 5.14 ( 2162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8598 (m-80) cc_final: 0.8246 (m-80) REVERT: E 287 GLU cc_start: 0.9000 (pt0) cc_final: 0.8780 (pt0) REVERT: E 289 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7926 (tm-30) REVERT: E 404 MET cc_start: 0.8301 (mmm) cc_final: 0.8042 (tpp) REVERT: E 424 ASP cc_start: 0.8435 (p0) cc_final: 0.8103 (p0) REVERT: F 203 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8048 (mt0) REVERT: F 316 MET cc_start: 0.9320 (mtm) cc_final: 0.8937 (mtp) REVERT: F 442 MET cc_start: 0.6147 (tmm) cc_final: 0.5035 (ttt) REVERT: F 488 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8728 (tp) REVERT: C 28 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: C 171 HIS cc_start: 0.8928 (t-90) cc_final: 0.8548 (t-90) REVERT: C 274 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7792 (pm20) REVERT: C 276 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8452 (mm-30) REVERT: D 116 ASP cc_start: 0.8536 (t0) cc_final: 0.8232 (t70) REVERT: D 161 ASP cc_start: 0.9084 (m-30) cc_final: 0.8770 (m-30) outliers start: 26 outliers final: 15 residues processed: 126 average time/residue: 0.0877 time to fit residues: 17.1670 Evaluate side-chains 122 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain D residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 chunk 135 optimal weight: 0.2980 chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.118376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085395 restraints weight = 36246.812| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.95 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12954 Z= 0.134 Angle : 0.566 9.584 17737 Z= 0.304 Chirality : 0.041 0.216 2004 Planarity : 0.004 0.050 2080 Dihedral : 18.117 61.541 2158 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 2.33 % Allowed : 11.72 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1421 helix: 2.08 (0.17), residues: 850 sheet: -0.68 (0.55), residues: 83 loop : 0.25 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 219 TYR 0.014 0.001 TYR E 237 PHE 0.013 0.001 PHE C 221 TRP 0.012 0.001 TRP F 230 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (12954) covalent geometry : angle 0.56600 / 0.30 (17737) hydrogen bonds : bond 0.04166 / 4.51 ( 751) hydrogen bonds : angle 4.24747 / 5.07 ( 2162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8630 (m-80) cc_final: 0.8382 (m-80) REVERT: E 287 GLU cc_start: 0.8841 (pt0) cc_final: 0.8612 (pt0) REVERT: E 389 GLU cc_start: 0.8650 (mp0) cc_final: 0.8250 (mp0) REVERT: E 404 MET cc_start: 0.8113 (mmm) cc_final: 0.7783 (tpp) REVERT: E 424 ASP cc_start: 0.8355 (p0) cc_final: 0.8009 (p0) REVERT: F 203 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7808 (mt0) REVERT: F 316 MET cc_start: 0.9177 (mtm) cc_final: 0.8770 (mtm) REVERT: F 442 MET cc_start: 0.6196 (tmm) cc_final: 0.5974 (tmm) REVERT: F 473 GLU cc_start: 0.8786 (tp30) cc_final: 0.8386 (tp30) REVERT: F 488 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 171 HIS cc_start: 0.8845 (t-90) cc_final: 0.8493 (t-90) REVERT: C 209 GLU cc_start: 0.8011 (pm20) cc_final: 0.7747 (pm20) REVERT: C 274 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: C 276 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: D 161 ASP cc_start: 0.9009 (m-30) cc_final: 0.8619 (m-30) outliers start: 30 outliers final: 17 residues processed: 124 average time/residue: 0.0947 time to fit residues: 18.4880 Evaluate side-chains 120 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain D residue 81 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.118382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.085415 restraints weight = 36466.961| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.98 r_work: 0.3421 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12954 Z= 0.127 Angle : 0.556 9.388 17737 Z= 0.301 Chirality : 0.040 0.205 2004 Planarity : 0.004 0.050 2080 Dihedral : 18.059 61.018 2158 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 1.94 % Allowed : 11.96 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.23), residues: 1421 helix: 2.11 (0.17), residues: 854 sheet: -0.63 (0.56), residues: 83 loop : 0.26 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 472 TYR 0.013 0.001 TYR D 32 PHE 0.030 0.001 PHE C 99 TRP 0.012 0.001 TRP F 230 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (12954) covalent geometry : angle 0.55633 / 0.30 (17737) hydrogen bonds : bond 0.04068 / 4.40 ( 751) hydrogen bonds : angle 4.21538 / 5.08 ( 2162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8672 (m-80) cc_final: 0.8375 (m-80) REVERT: E 242 MET cc_start: 0.8572 (mmm) cc_final: 0.8354 (tpt) REVERT: E 287 GLU cc_start: 0.9004 (pt0) cc_final: 0.8781 (pt0) REVERT: E 389 GLU cc_start: 0.8938 (mp0) cc_final: 0.8636 (mp0) REVERT: E 404 MET cc_start: 0.8235 (mmm) cc_final: 0.7888 (tpp) REVERT: E 424 ASP cc_start: 0.8396 (p0) cc_final: 0.8121 (p0) REVERT: F 203 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8150 (mt0) REVERT: F 488 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 171 HIS cc_start: 0.8934 (t-90) cc_final: 0.8551 (t-90) REVERT: C 209 GLU cc_start: 0.8123 (pm20) cc_final: 0.7912 (pm20) REVERT: D 161 ASP cc_start: 0.9083 (m-30) cc_final: 0.8823 (m-30) outliers start: 25 outliers final: 17 residues processed: 125 average time/residue: 0.0922 time to fit residues: 18.2191 Evaluate side-chains 119 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 291 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 14 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.117347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084362 restraints weight = 36224.668| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.97 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12954 Z= 0.151 Angle : 0.573 11.995 17737 Z= 0.308 Chirality : 0.041 0.206 2004 Planarity : 0.004 0.049 2080 Dihedral : 18.065 60.839 2158 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 2.02 % Allowed : 12.34 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.23), residues: 1421 helix: 2.15 (0.17), residues: 851 sheet: -0.61 (0.53), residues: 93 loop : 0.15 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 318 TYR 0.014 0.001 TYR D 32 PHE 0.012 0.001 PHE C 99 TRP 0.011 0.001 TRP F 526 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12954) covalent geometry : angle 0.57259 / 0.31 (17737) hydrogen bonds : bond 0.04103 / 4.45 ( 751) hydrogen bonds : angle 4.22145 / 5.06 ( 2162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8674 (m-80) cc_final: 0.8416 (m-80) REVERT: E 242 MET cc_start: 0.8211 (mmm) cc_final: 0.7944 (tpt) REVERT: E 289 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7823 (tm-30) REVERT: E 389 GLU cc_start: 0.8656 (mp0) cc_final: 0.8251 (mp0) REVERT: E 404 MET cc_start: 0.8106 (mmm) cc_final: 0.7785 (tpp) REVERT: E 424 ASP cc_start: 0.8344 (p0) cc_final: 0.8030 (p0) REVERT: F 203 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7965 (mt0) REVERT: F 442 MET cc_start: 0.6166 (tmm) cc_final: 0.5341 (ttt) REVERT: C 171 HIS cc_start: 0.8814 (t-90) cc_final: 0.8415 (t-90) REVERT: C 276 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: D 160 GLN cc_start: 0.8838 (mp10) cc_final: 0.8612 (tp-100) REVERT: D 161 ASP cc_start: 0.9083 (m-30) cc_final: 0.8678 (m-30) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.1024 time to fit residues: 19.0796 Evaluate side-chains 118 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.0020 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.117906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085129 restraints weight = 36146.919| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.91 r_work: 0.3403 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12954 Z= 0.137 Angle : 0.578 11.980 17737 Z= 0.310 Chirality : 0.041 0.208 2004 Planarity : 0.004 0.051 2080 Dihedral : 18.054 60.708 2158 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 1.94 % Allowed : 12.19 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.23), residues: 1421 helix: 2.15 (0.17), residues: 853 sheet: -0.55 (0.52), residues: 95 loop : 0.17 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 472 TYR 0.014 0.001 TYR D 32 PHE 0.017 0.001 PHE C 99 TRP 0.012 0.001 TRP F 526 HIS 0.013 0.001 HIS F 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (12954) covalent geometry : angle 0.57757 / 0.31 (17737) hydrogen bonds : bond 0.04052 / 4.39 ( 751) hydrogen bonds : angle 4.21448 / 5.03 ( 2162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8647 (m-80) cc_final: 0.8434 (m-80) REVERT: E 242 MET cc_start: 0.8612 (mmm) cc_final: 0.8368 (tpt) REVERT: E 389 GLU cc_start: 0.8915 (mp0) cc_final: 0.8578 (mp0) REVERT: E 404 MET cc_start: 0.8115 (mmm) cc_final: 0.7878 (tpp) REVERT: E 424 ASP cc_start: 0.8293 (p0) cc_final: 0.8050 (p0) REVERT: F 203 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8108 (mt0) REVERT: F 219 ARG cc_start: 0.8566 (tpt170) cc_final: 0.8309 (tpp-160) REVERT: F 442 MET cc_start: 0.5837 (tmm) cc_final: 0.5171 (ttt) REVERT: C 171 HIS cc_start: 0.8889 (t-90) cc_final: 0.8497 (t-90) REVERT: D 160 GLN cc_start: 0.8970 (mp10) cc_final: 0.8591 (tp-100) REVERT: D 161 ASP cc_start: 0.9160 (m-30) cc_final: 0.8865 (m-30) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.1047 time to fit residues: 18.7911 Evaluate side-chains 119 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 67 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 3 optimal weight: 20.0000 chunk 127 optimal weight: 0.0770 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.117560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084632 restraints weight = 36553.625| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.95 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12954 Z= 0.139 Angle : 0.580 11.661 17737 Z= 0.311 Chirality : 0.041 0.202 2004 Planarity : 0.004 0.055 2080 Dihedral : 18.045 60.541 2158 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.63 % Allowed : 12.73 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.23), residues: 1421 helix: 2.13 (0.17), residues: 853 sheet: -0.44 (0.53), residues: 91 loop : 0.13 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 472 TYR 0.017 0.001 TYR E 237 PHE 0.014 0.001 PHE C 99 TRP 0.011 0.001 TRP F 526 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12954) covalent geometry : angle 0.57964 / 0.31 (17737) hydrogen bonds : bond 0.04045 / 4.41 ( 751) hydrogen bonds : angle 4.22897 / 5.04 ( 2162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8589 (m-80) cc_final: 0.8378 (m-80) REVERT: E 242 MET cc_start: 0.8207 (mmm) cc_final: 0.7918 (tpt) REVERT: E 389 GLU cc_start: 0.8647 (mp0) cc_final: 0.8220 (mp0) REVERT: E 404 MET cc_start: 0.8033 (mmm) cc_final: 0.7742 (tpp) REVERT: E 424 ASP cc_start: 0.8283 (p0) cc_final: 0.8016 (p0) REVERT: F 203 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7927 (mt0) REVERT: F 442 MET cc_start: 0.6037 (tmm) cc_final: 0.5296 (ttt) REVERT: C 171 HIS cc_start: 0.8838 (t-90) cc_final: 0.8432 (t-90) REVERT: C 209 GLU cc_start: 0.7988 (pm20) cc_final: 0.7753 (pm20) REVERT: C 276 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8321 (tp30) REVERT: D 160 GLN cc_start: 0.8844 (mp10) cc_final: 0.8542 (tp-100) REVERT: D 161 ASP cc_start: 0.9114 (m-30) cc_final: 0.8732 (m-30) outliers start: 21 outliers final: 19 residues processed: 114 average time/residue: 0.1024 time to fit residues: 17.9899 Evaluate side-chains 118 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 226 GLN Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 357 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.117483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084673 restraints weight = 36467.355| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 3.94 r_work: 0.3394 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12954 Z= 0.135 Angle : 0.580 11.464 17737 Z= 0.311 Chirality : 0.040 0.202 2004 Planarity : 0.004 0.051 2080 Dihedral : 18.030 60.414 2158 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.48 % Allowed : 12.97 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1421 helix: 2.15 (0.17), residues: 851 sheet: -0.54 (0.53), residues: 89 loop : 0.17 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 295 TYR 0.015 0.001 TYR E 237 PHE 0.014 0.001 PHE C 99 TRP 0.012 0.001 TRP F 526 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12954) covalent geometry : angle 0.57957 / 0.31 (17737) hydrogen bonds : bond 0.04023 / 4.37 ( 751) hydrogen bonds : angle 4.19134 / 4.99 ( 2162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.93 seconds wall clock time: 56 minutes 8.18 seconds (3368.18 seconds total)