Starting phenix.real_space_refine on Sun Apr 5 19:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxh_64583/04_2026/9uxh_64583.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxh_64583/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9uxh_64583/04_2026/9uxh_64583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxh_64583/04_2026/9uxh_64583.map" model { file = "/net/cci-nas-00/data/ceres_data/9uxh_64583/04_2026/9uxh_64583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxh_64583/04_2026/9uxh_64583.cif" } 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-2.1rc1-6017/lib/python3.9/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: 3.01, per 1000 atoms: 0.24 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: 1.08 Conformation dependent library (CDL) restraints added in 586.3 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: 1.76 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: 2.53 Time building geometry restraints manager: 1.45 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=" N SER C 32 " pdb=" CA SER C 32 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.56e-02 4.11e+03 2.49e+00 bond pdb=" CA ASN C 31 " pdb=" C ASN C 31 " ideal model delta sigma weight residual 1.526 1.547 -0.021 1.37e-02 5.33e+03 2.26e+00 bond pdb=" CG PHE C 221 " pdb=" CD1 PHE C 221 " ideal model delta sigma weight residual 1.384 1.353 0.031 2.10e-02 2.27e+03 2.23e+00 bond pdb=" C ARG C 224 " pdb=" N LEU C 225 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.49e-02 4.50e+03 1.96e+00 bond pdb=" CB VAL C 216 " pdb=" CG2 VAL C 216 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 17553 2.56 - 5.12: 163 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=" CB LEU C 225 " pdb=" CG LEU C 225 " pdb=" CD2 LEU C 225 " ideal model delta sigma weight residual 110.70 123.10 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" N GLY C 48 " pdb=" CA GLY C 48 " pdb=" C GLY C 48 " ideal model delta sigma weight residual 113.18 122.61 -9.43 2.37e+00 1.78e-01 1.58e+01 angle pdb=" C LEU C 225 " pdb=" CA LEU C 225 " pdb=" CB LEU C 225 " ideal model delta sigma weight residual 109.99 101.82 8.17 2.09e+00 2.29e-01 1.53e+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: 1945 0.101 - 0.201: 56 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: 5.420 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.660 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.003 0.045 12954 Z= 0.156 Angle : 0.631 12.797 17737 Z= 0.335 Chirality : 0.042 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 covalent geometry : bond 0.00334 (12954) covalent geometry : angle 0.63139 (17737) hydrogen bonds : bond 0.14049 ( 751) hydrogen bonds : angle 5.73486 ( 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 : 0.470 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: 0.8377 (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: 0.1367 time to fit residues: 40.9048 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 : 0.461 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** F 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 343 GLN F 347 ASN F 508 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.118365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085662 restraints weight = 36338.192| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.93 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12954 Z= 0.198 Angle : 0.655 11.206 17737 Z= 0.351 Chirality : 0.043 0.280 2004 Planarity : 0.004 0.047 2080 Dihedral : 18.220 67.476 2162 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.40 % Allowed : 8.15 % Favored : 90.45 % 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: 1.93 (0.23), residues: 1421 helix: 1.98 (0.17), residues: 845 sheet: 0.07 (0.54), residues: 93 loop : 0.39 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 476 TYR 0.018 0.002 TYR D 32 PHE 0.029 0.002 PHE C 241 TRP 0.021 0.002 TRP F 526 HIS 0.006 0.001 HIS F 508 Details of bonding type rmsd covalent geometry : bond 0.00442 (12954) covalent geometry : angle 0.65527 (17737) hydrogen bonds : bond 0.04628 ( 751) hydrogen bonds : angle 4.55148 ( 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 144 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8275 (m-80) cc_final: 0.7913 (m-80) REVERT: E 284 TYR cc_start: 0.8037 (t80) cc_final: 0.7797 (t80) REVERT: E 287 GLU cc_start: 0.8824 (pt0) cc_final: 0.8584 (pt0) REVERT: E 424 ASP cc_start: 0.8420 (p0) cc_final: 0.8165 (p0) REVERT: F 203 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7862 (mt0) REVERT: F 211 GLU cc_start: 0.9261 (tp30) cc_final: 0.9021 (tp30) REVERT: F 454 GLU cc_start: 0.8530 (tt0) cc_final: 0.8329 (tt0) REVERT: F 473 GLU cc_start: 0.8798 (tp30) cc_final: 0.8383 (tp30) REVERT: C 28 GLU cc_start: 0.8745 (mp0) cc_final: 0.8388 (mm-30) REVERT: C 171 HIS cc_start: 0.8766 (t-90) cc_final: 0.8360 (t-90) REVERT: C 220 ASP cc_start: 0.9015 (t70) cc_final: 0.8766 (p0) REVERT: C 283 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8504 (mp) REVERT: D 116 ASP cc_start: 0.8251 (t0) cc_final: 0.7910 (t70) REVERT: D 161 ASP cc_start: 0.8984 (m-30) cc_final: 0.8664 (m-30) outliers start: 18 outliers final: 10 residues processed: 142 average time/residue: 0.1001 time to fit residues: 21.5868 Evaluate side-chains 116 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 421 LEU 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 221 PHE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 134 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 19 optimal weight: 0.0270 chunk 123 optimal weight: 0.9980 chunk 103 optimal weight: 0.0050 chunk 46 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 410 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.119757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.087149 restraints weight = 36696.859| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.93 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12954 Z= 0.134 Angle : 0.583 9.355 17737 Z= 0.312 Chirality : 0.040 0.268 2004 Planarity : 0.004 0.048 2080 Dihedral : 17.898 61.761 2158 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.71 % Allowed : 10.09 % Favored : 88.20 % 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: 2.08 (0.17), residues: 853 sheet: -0.16 (0.52), residues: 93 loop : 0.23 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 295 TYR 0.014 0.001 TYR D 32 PHE 0.021 0.001 PHE C 53 TRP 0.016 0.002 TRP F 230 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00288 (12954) covalent geometry : angle 0.58341 (17737) hydrogen bonds : bond 0.04202 ( 751) hydrogen bonds : angle 4.36202 ( 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 143 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 284 TYR cc_start: 0.7937 (t80) cc_final: 0.7732 (t80) REVERT: E 287 GLU cc_start: 0.8824 (pt0) cc_final: 0.8585 (pt0) REVERT: E 424 ASP cc_start: 0.8412 (p0) cc_final: 0.8020 (p0) REVERT: F 203 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7825 (mt0) REVERT: F 473 GLU cc_start: 0.8794 (tp30) cc_final: 0.8372 (tp30) REVERT: F 509 GLU cc_start: 0.7501 (pm20) cc_final: 0.7206 (pm20) REVERT: C 28 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8391 (mm-30) REVERT: C 171 HIS cc_start: 0.8813 (t-90) cc_final: 0.8402 (t-90) REVERT: C 220 ASP cc_start: 0.8997 (t70) cc_final: 0.8795 (p0) REVERT: D 116 ASP cc_start: 0.8231 (t0) cc_final: 0.7900 (t70) REVERT: D 161 ASP cc_start: 0.8977 (m-30) cc_final: 0.8643 (m-30) outliers start: 22 outliers final: 10 residues processed: 136 average time/residue: 0.1026 time to fit residues: 21.3244 Evaluate side-chains 117 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 623 HIS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 47 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 45 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4217 r_free = 0.4217 target = 0.118075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.085302 restraints weight = 36296.359| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.88 r_work: 0.3350 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12954 Z= 0.150 Angle : 0.572 8.883 17737 Z= 0.306 Chirality : 0.041 0.294 2004 Planarity : 0.004 0.048 2080 Dihedral : 17.846 61.521 2158 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % 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: 1.99 (0.23), residues: 1421 helix: 2.13 (0.17), residues: 848 sheet: -0.27 (0.56), residues: 83 loop : 0.25 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 476 TYR 0.015 0.001 TYR D 32 PHE 0.015 0.001 PHE C 53 TRP 0.010 0.001 TRP F 526 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00327 (12954) covalent geometry : angle 0.57204 (17737) hydrogen bonds : bond 0.04090 ( 751) hydrogen bonds : angle 4.26358 ( 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 138 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8560 (m-80) cc_final: 0.8256 (m-80) REVERT: E 289 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7911 (tm-30) REVERT: E 389 GLU cc_start: 0.8929 (mp0) cc_final: 0.8594 (mp0) REVERT: E 415 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7511 (mtt-85) REVERT: E 424 ASP cc_start: 0.8375 (p0) cc_final: 0.8090 (p0) REVERT: F 203 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8101 (mt0) REVERT: F 509 GLU cc_start: 0.7751 (pm20) cc_final: 0.7436 (pm20) REVERT: C 28 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8415 (mm-30) REVERT: C 171 HIS cc_start: 0.8907 (t-90) cc_final: 0.8534 (t-90) REVERT: C 220 ASP cc_start: 0.9109 (t70) cc_final: 0.8909 (p0) REVERT: C 274 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8309 (pm20) REVERT: D 11 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8115 (tm-30) REVERT: D 116 ASP cc_start: 0.8545 (t0) cc_final: 0.8242 (t70) REVERT: D 161 ASP cc_start: 0.9069 (m-30) cc_final: 0.8839 (m-30) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.0991 time to fit residues: 19.5882 Evaluate side-chains 117 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 586 LEU 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 197 LEU Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 291 GLU 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: 0.7980 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4169 r_free = 0.4169 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.082249 restraints weight = 37120.712| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.04 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12954 Z= 0.135 Angle : 0.553 9.572 17737 Z= 0.297 Chirality : 0.040 0.257 2004 Planarity : 0.004 0.052 2080 Dihedral : 17.786 61.153 2158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 2.02 % Allowed : 11.80 % Favored : 86.18 % 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: 2.00 (0.23), residues: 1421 helix: 2.20 (0.17), residues: 850 sheet: -0.41 (0.52), residues: 93 loop : 0.18 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 415 TYR 0.014 0.001 TYR D 32 PHE 0.012 0.001 PHE C 221 TRP 0.010 0.001 TRP F 230 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00294 (12954) covalent geometry : angle 0.55268 (17737) hydrogen bonds : bond 0.03966 ( 751) hydrogen bonds : angle 4.18122 ( 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 141 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.424 Fit side-chains REVERT: E 237 TYR cc_start: 0.8527 (m-80) cc_final: 0.8088 (m-80) REVERT: E 289 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7792 (tm-30) REVERT: E 389 GLU cc_start: 0.8618 (mp0) cc_final: 0.8222 (mp0) REVERT: E 424 ASP cc_start: 0.8347 (p0) cc_final: 0.8045 (p0) REVERT: F 203 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7872 (mt0) REVERT: F 509 GLU cc_start: 0.7574 (pm20) cc_final: 0.7369 (pm20) REVERT: C 171 HIS cc_start: 0.8832 (t-90) cc_final: 0.8486 (t-90) REVERT: C 209 GLU cc_start: 0.7870 (pm20) cc_final: 0.7533 (pm20) REVERT: C 274 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: D 88 SER cc_start: 0.9274 (t) cc_final: 0.9072 (p) REVERT: D 116 ASP cc_start: 0.8280 (t0) cc_final: 0.7974 (t70) REVERT: D 161 ASP cc_start: 0.9075 (m-30) cc_final: 0.8715 (m-30) outliers start: 26 outliers final: 11 residues processed: 131 average time/residue: 0.0998 time to fit residues: 20.2464 Evaluate side-chains 115 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 THR 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 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 526 TRP Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain D residue 81 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 28 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4197 r_free = 0.4197 target = 0.117431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.083864 restraints weight = 36499.813| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 3.94 r_work: 0.3398 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12954 Z= 0.138 Angle : 0.568 11.691 17737 Z= 0.301 Chirality : 0.040 0.235 2004 Planarity : 0.004 0.051 2080 Dihedral : 17.766 60.921 2158 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.86 % Allowed : 12.73 % Favored : 85.40 % 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: 2.03 (0.23), residues: 1421 helix: 2.21 (0.17), residues: 852 sheet: -0.38 (0.53), residues: 93 loop : 0.21 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 472 TYR 0.015 0.001 TYR D 32 PHE 0.016 0.001 PHE C 221 TRP 0.011 0.001 TRP F 230 HIS 0.004 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00302 (12954) covalent geometry : angle 0.56796 (17737) hydrogen bonds : bond 0.03970 ( 751) hydrogen bonds : angle 4.16165 ( 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 137 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8526 (m-80) cc_final: 0.8180 (m-80) REVERT: E 289 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7882 (tm-30) REVERT: E 389 GLU cc_start: 0.8913 (mp0) cc_final: 0.8543 (mp0) REVERT: E 415 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7554 (mtt-85) REVERT: E 424 ASP cc_start: 0.8348 (p0) cc_final: 0.8145 (p0) REVERT: F 203 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8179 (mt0) REVERT: C 171 HIS cc_start: 0.8926 (t-90) cc_final: 0.8529 (t-90) REVERT: C 274 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: D 54 TYR cc_start: 0.9050 (m-80) cc_final: 0.8786 (m-80) REVERT: D 61 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8908 (tp) REVERT: D 161 ASP cc_start: 0.9155 (m-30) cc_final: 0.8869 (m-30) outliers start: 24 outliers final: 12 residues processed: 128 average time/residue: 0.1096 time to fit residues: 21.2770 Evaluate side-chains 115 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 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 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 526 TRP Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 61 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 0.0000 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4217 r_free = 0.4217 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084949 restraints weight = 36529.704| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 3.99 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3453 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= 0.133 Angle : 0.574 11.553 17737 Z= 0.307 Chirality : 0.040 0.232 2004 Planarity : 0.004 0.051 2080 Dihedral : 17.748 60.652 2158 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.55 % Allowed : 13.43 % Favored : 85.02 % 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: 2.11 (0.23), residues: 1421 helix: 2.24 (0.17), residues: 848 sheet: -0.12 (0.54), residues: 91 loop : 0.25 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 419 TYR 0.014 0.001 TYR D 32 PHE 0.018 0.001 PHE C 221 TRP 0.010 0.001 TRP F 526 HIS 0.005 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00289 (12954) covalent geometry : angle 0.57384 (17737) hydrogen bonds : bond 0.03892 ( 751) hydrogen bonds : angle 4.16086 ( 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 136 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8540 (m-80) cc_final: 0.8224 (m-80) REVERT: E 289 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7790 (tm-30) REVERT: E 389 GLU cc_start: 0.8639 (mp0) cc_final: 0.8195 (mp0) REVERT: E 424 ASP cc_start: 0.8335 (p0) cc_final: 0.8068 (p0) REVERT: F 203 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8008 (mt0) REVERT: F 479 LYS cc_start: 0.9030 (mmpt) cc_final: 0.8710 (ttpp) REVERT: F 509 GLU cc_start: 0.7619 (pm20) cc_final: 0.7320 (pm20) REVERT: C 171 HIS cc_start: 0.8844 (t-90) cc_final: 0.8437 (t-90) REVERT: C 209 GLU cc_start: 0.7852 (pm20) cc_final: 0.7550 (pm20) REVERT: C 211 ARG cc_start: 0.8711 (mpp80) cc_final: 0.8467 (mtm180) REVERT: D 160 GLN cc_start: 0.8873 (mp10) cc_final: 0.8596 (tp-100) REVERT: D 161 ASP cc_start: 0.9112 (m-30) cc_final: 0.8729 (m-30) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.1089 time to fit residues: 20.8964 Evaluate side-chains 118 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 81 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 14 optimal weight: 4.9990 chunk 140 optimal weight: 0.0870 chunk 131 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 139 optimal weight: 0.0270 chunk 50 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4193 r_free = 0.4193 target = 0.116818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.083689 restraints weight = 36204.740| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.93 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12954 Z= 0.150 Angle : 0.583 10.356 17737 Z= 0.310 Chirality : 0.040 0.247 2004 Planarity : 0.004 0.049 2080 Dihedral : 17.756 61.311 2158 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 1.79 % Allowed : 13.35 % Favored : 84.86 % 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: 2.07 (0.23), residues: 1421 helix: 2.20 (0.18), residues: 855 sheet: -0.15 (0.53), residues: 93 loop : 0.24 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 472 TYR 0.014 0.001 TYR D 32 PHE 0.031 0.001 PHE C 221 TRP 0.012 0.001 TRP F 534 HIS 0.009 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00334 (12954) covalent geometry : angle 0.58346 (17737) hydrogen bonds : bond 0.03943 ( 751) hydrogen bonds : angle 4.15111 ( 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 125 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8588 (m-80) cc_final: 0.8224 (m-80) REVERT: E 242 MET cc_start: 0.8235 (mmm) cc_final: 0.7991 (tpt) REVERT: E 289 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7814 (tm-30) REVERT: E 389 GLU cc_start: 0.8597 (mp0) cc_final: 0.8003 (mp0) REVERT: E 424 ASP cc_start: 0.8235 (p0) cc_final: 0.7995 (p0) REVERT: F 203 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7957 (mt0) REVERT: C 171 HIS cc_start: 0.8882 (t-90) cc_final: 0.8488 (t-90) REVERT: C 209 GLU cc_start: 0.7804 (pm20) cc_final: 0.7543 (pm20) REVERT: C 211 ARG cc_start: 0.8783 (mpp80) cc_final: 0.8540 (mtm180) REVERT: C 274 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8001 (pm20) REVERT: D 161 ASP cc_start: 0.9155 (m-30) cc_final: 0.8742 (m-30) outliers start: 23 outliers final: 14 residues processed: 118 average time/residue: 0.1072 time to fit residues: 19.1614 Evaluate side-chains 113 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 110 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 274 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: 0.0020 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4211 r_free = 0.4211 target = 0.117573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084701 restraints weight = 36241.480| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 3.95 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12954 Z= 0.136 Angle : 0.576 10.808 17737 Z= 0.306 Chirality : 0.040 0.240 2004 Planarity : 0.004 0.050 2080 Dihedral : 17.731 62.086 2158 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.40 % Allowed : 13.43 % Favored : 85.17 % 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: 2.05 (0.23), residues: 1421 helix: 2.20 (0.18), residues: 855 sheet: -0.27 (0.52), residues: 93 loop : 0.22 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 472 TYR 0.013 0.001 TYR E 284 PHE 0.022 0.001 PHE C 221 TRP 0.012 0.001 TRP F 534 HIS 0.010 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00301 (12954) covalent geometry : angle 0.57609 (17737) hydrogen bonds : bond 0.03825 ( 751) hydrogen bonds : angle 4.12971 ( 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 123 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8570 (m-80) cc_final: 0.8223 (m-80) REVERT: E 242 MET cc_start: 0.8230 (mmm) cc_final: 0.7988 (tpt) REVERT: E 289 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7799 (tm-30) REVERT: E 389 GLU cc_start: 0.8596 (mp0) cc_final: 0.8148 (mp0) REVERT: E 424 ASP cc_start: 0.8182 (p0) cc_final: 0.7958 (p0) REVERT: F 203 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7945 (mt0) REVERT: F 479 LYS cc_start: 0.9069 (mmpt) cc_final: 0.8707 (ttpp) REVERT: C 171 HIS cc_start: 0.8896 (t-90) cc_final: 0.8502 (t-90) REVERT: C 209 GLU cc_start: 0.7869 (pm20) cc_final: 0.7566 (pm20) REVERT: C 211 ARG cc_start: 0.8716 (mpp80) cc_final: 0.8482 (mtm180) REVERT: D 54 TYR cc_start: 0.8768 (m-80) cc_final: 0.8522 (m-80) REVERT: D 160 GLN cc_start: 0.8923 (mp10) cc_final: 0.8633 (tp-100) REVERT: D 161 ASP cc_start: 0.9135 (m-30) cc_final: 0.8711 (m-30) outliers start: 18 outliers final: 13 residues processed: 118 average time/residue: 0.1072 time to fit residues: 18.9181 Evaluate side-chains 112 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 357 ILE 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 110 GLN Chi-restraints excluded: chain C residue 197 LEU 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 67 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 0.0470 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4177 r_free = 0.4177 target = 0.116478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082389 restraints weight = 36595.904| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.00 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12954 Z= 0.138 Angle : 0.596 10.674 17737 Z= 0.315 Chirality : 0.041 0.324 2004 Planarity : 0.004 0.049 2080 Dihedral : 17.736 65.110 2158 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 13.66 % Favored : 85.09 % 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: 2.05 (0.23), residues: 1421 helix: 2.20 (0.17), residues: 856 sheet: -0.31 (0.52), residues: 93 loop : 0.23 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 415 TYR 0.019 0.001 TYR E 284 PHE 0.031 0.001 PHE C 221 TRP 0.012 0.001 TRP F 534 HIS 0.010 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00307 (12954) covalent geometry : angle 0.59591 (17737) hydrogen bonds : bond 0.03824 ( 751) hydrogen bonds : angle 4.12751 ( 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 119 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 237 TYR cc_start: 0.8582 (m-80) cc_final: 0.8245 (m-80) REVERT: E 242 MET cc_start: 0.8226 (mmm) cc_final: 0.7974 (tpt) REVERT: E 289 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7824 (tm-30) REVERT: E 389 GLU cc_start: 0.8610 (mp0) cc_final: 0.8177 (mp0) REVERT: F 203 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7980 (mt0) REVERT: F 479 LYS cc_start: 0.9084 (mmpt) cc_final: 0.8704 (ttpp) REVERT: F 509 GLU cc_start: 0.7592 (pm20) cc_final: 0.7302 (pm20) REVERT: C 171 HIS cc_start: 0.8879 (t-90) cc_final: 0.8487 (t-90) REVERT: C 209 GLU cc_start: 0.7888 (pm20) cc_final: 0.7620 (pm20) REVERT: C 211 ARG cc_start: 0.8765 (mpp80) cc_final: 0.8534 (mtm180) REVERT: D 54 TYR cc_start: 0.8798 (m-80) cc_final: 0.8591 (m-80) REVERT: D 156 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8471 (mt-10) REVERT: D 160 GLN cc_start: 0.8917 (mp10) cc_final: 0.8683 (tp-100) REVERT: D 161 ASP cc_start: 0.9147 (m-30) cc_final: 0.8726 (m-30) outliers start: 16 outliers final: 15 residues processed: 114 average time/residue: 0.1093 time to fit residues: 18.6664 Evaluate side-chains 113 residues out of total 1288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 498 THR Chi-restraints excluded: chain F residue 526 TRP Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 586 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 81 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4156 r_free = 0.4156 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082196 restraints weight = 36336.078| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.83 r_work: 0.3384 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4035 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= 0.153 Angle : 0.600 10.591 17737 Z= 0.317 Chirality : 0.041 0.303 2004 Planarity : 0.004 0.049 2080 Dihedral : 17.792 67.634 2158 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.96 % Favored : 96.97 % Rotamer: Outliers : 1.32 % Allowed : 13.66 % Favored : 85.02 % 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: 2.04 (0.23), residues: 1421 helix: 2.19 (0.17), residues: 856 sheet: -0.32 (0.52), residues: 93 loop : 0.23 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 415 TYR 0.020 0.001 TYR E 284 PHE 0.024 0.001 PHE C 221 TRP 0.014 0.001 TRP F 534 HIS 0.010 0.001 HIS C 180 Details of bonding type rmsd covalent geometry : bond 0.00344 (12954) covalent geometry : angle 0.60012 (17737) hydrogen bonds : bond 0.03875 ( 751) hydrogen bonds : angle 4.12622 ( 2162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.82 seconds wall clock time: 58 minutes 44.59 seconds (3524.59 seconds total)