Starting phenix.real_space_refine on Wed Aug 5 17:04:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewz_50027/08_2026/9ewz_50027.cif" } resolution = 2.22 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 1 5.21 5 S 43 5.16 5 C 6697 2.51 5 N 1853 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10780 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9728 Classifications: {'peptide': 1205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1164} Chain: "B" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 502 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 2.41, per 1000 atoms: 0.22 Number of scatterers: 10780 At special positions: 0 Unit cell: (78.44, 110.26, 129.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 43 16.00 P 50 15.00 Mg 1 11.99 O 2136 8.00 N 1853 7.00 C 6697 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: 1.02 Conformation dependent library (CDL) restraints added in 372.0 milliseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 58.5% alpha, 6.6% beta 24 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 3 through 28 Proline residue: C 11 - end of helix Processing helix chain 'C' and resid 61 through 75 removed outlier: 3.560A pdb=" N GLU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 101 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 137 through 148 removed outlier: 3.727A pdb=" N LEU C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 168 removed outlier: 3.588A pdb=" N LEU C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 185 removed outlier: 3.508A pdb=" N LEU C 185 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 203 removed outlier: 4.398A pdb=" N GLY C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.530A pdb=" N TRP C 208 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 209 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLN C 210 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 4.020A pdb=" N GLY C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 235 through 243 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 248 through 258 removed outlier: 3.522A pdb=" N ASN C 258 " --> pdb=" O TYR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 268 removed outlier: 3.803A pdb=" N THR C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.822A pdb=" N ILE C 307 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 335 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 340 through 349 removed outlier: 3.504A pdb=" N LEU C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 375 removed outlier: 3.870A pdb=" N ASP C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 405 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.715A pdb=" N HIS C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 424 removed outlier: 4.163A pdb=" N ALA C 424 " --> pdb=" O GLN C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.664A pdb=" N LEU C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 459 through 474 Processing helix chain 'C' and resid 478 through 500 Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 518 through 529 Processing helix chain 'C' and resid 535 through 545 removed outlier: 4.142A pdb=" N PHE C 545 " --> pdb=" O MET C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 565 removed outlier: 3.911A pdb=" N PHE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.663A pdb=" N ASN C 578 " --> pdb=" O TRP C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 636 Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 662 through 671 removed outlier: 3.578A pdb=" N LYS C 671 " --> pdb=" O ASN C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 677 No H-bonds generated for 'chain 'C' and resid 675 through 677' Processing helix chain 'C' and resid 688 through 692 Processing helix chain 'C' and resid 697 through 699 No H-bonds generated for 'chain 'C' and resid 697 through 699' Processing helix chain 'C' and resid 700 through 704 removed outlier: 3.541A pdb=" N SER C 703 " --> pdb=" O SER C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 746 Processing helix chain 'C' and resid 752 through 756 Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 808 through 819 Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 838 through 856 removed outlier: 4.124A pdb=" N ASP C 842 " --> pdb=" O ASN C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.693A pdb=" N GLU C 871 " --> pdb=" O LYS C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 910 removed outlier: 3.586A pdb=" N ILE C 908 " --> pdb=" O ILE C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 933 Processing helix chain 'C' and resid 941 through 962 Processing helix chain 'C' and resid 981 through 989 Processing helix chain 'C' and resid 1013 through 1027 Processing helix chain 'C' and resid 1030 through 1046 removed outlier: 4.042A pdb=" N TYR C1045 " --> pdb=" O SER C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1054 through 1066 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1104 through 1135 removed outlier: 4.530A pdb=" N VAL C1115 " --> pdb=" O THR C1111 " (cutoff:3.500A) Proline residue: C1116 - end of helix removed outlier: 3.627A pdb=" N ASP C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C1131 " --> pdb=" O ARG C1127 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C1134 " --> pdb=" O ASP C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1170 removed outlier: 4.341A pdb=" N ARG C1142 " --> pdb=" O GLY C1138 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C1148 " --> pdb=" O LYS C1144 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER C1149 " --> pdb=" O ARG C1145 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET C1170 " --> pdb=" O HIS C1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1178 Processing helix chain 'C' and resid 1179 through 1184 Processing helix chain 'C' and resid 1193 through 1199 Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46 removed outlier: 3.593A pdb=" N PHE C 55 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 387 through 389 removed outlier: 8.280A pdb=" N VAL C 388 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY C 352 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 309 " --> pdb=" O PHE C 351 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU C 353 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP C 311 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP C 503 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA C 555 " --> pdb=" O ASP C 503 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 505 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 557 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 507 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N MET C 559 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR C 602 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS C 586 " --> pdb=" O THR C 602 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 604 " --> pdb=" O MET C 584 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N MET C 584 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 606 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 618 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 679 through 680 Processing sheet with id=AA4, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.368A pdb=" N TYR C 732 " --> pdb=" O ILE C 717 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1001 through 1003 459 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2891 1.33 - 1.45: 2251 1.45 - 1.57: 5804 1.57 - 1.69: 98 1.69 - 1.81: 75 Bond restraints: 11119 Sorted by residual: bond pdb=" C2 SAM C1302 " pdb=" N3 SAM C1302 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" C3' DC B 3 " pdb=" C2' DC B 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.79e+00 bond pdb=" C8 SAM C1302 " pdb=" N7 SAM C1302 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C3' DA A 18 " pdb=" C2' DA A 18 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.34e+00 bond pdb=" C2 SAM C1302 " pdb=" N1 SAM C1302 " ideal model delta sigma weight residual 1.329 1.378 -0.049 2.00e-02 2.50e+03 6.00e+00 ... (remaining 11114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 14963 1.77 - 3.55: 255 3.55 - 5.32: 26 5.32 - 7.10: 5 7.10 - 8.87: 3 Bond angle restraints: 15252 Sorted by residual: angle pdb=" O4' DC A 14 " pdb=" C4' DC A 14 " pdb=" C3' DC A 14 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" N3 DT A 7 " pdb=" C4 DT A 7 " pdb=" O4 DT A 7 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT A 23 " pdb=" C4 DT A 23 " pdb=" O4 DT A 23 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT B 21 " pdb=" C4 DT B 21 " pdb=" O4 DT B 21 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT B 25 " pdb=" C4 DT B 25 " pdb=" O4 DT B 25 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 15247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 6277 34.06 - 68.12: 264 68.12 - 102.18: 4 102.18 - 136.23: 0 136.23 - 170.29: 4 Dihedral angle restraints: 6549 sinusoidal: 3023 harmonic: 3526 Sorted by residual: dihedral pdb=" C4' DC A 14 " pdb=" C3' DC A 14 " pdb=" O3' DC A 14 " pdb=" P DC A 15 " ideal model delta sinusoidal sigma weight residual 220.00 49.71 170.29 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC B 3 " pdb=" C3' DC B 3 " pdb=" O3' DC B 3 " pdb=" P DA B 4 " ideal model delta sinusoidal sigma weight residual 220.00 50.83 169.17 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA B 16 " pdb=" C3' DA B 16 " pdb=" O3' DA B 16 " pdb=" P DG B 17 " ideal model delta sinusoidal sigma weight residual 220.00 63.06 156.94 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 6546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1148 0.037 - 0.073: 377 0.073 - 0.110: 93 0.110 - 0.147: 28 0.147 - 0.183: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" C3' DA B 16 " pdb=" C4' DA B 16 " pdb=" O3' DA B 16 " pdb=" C2' DA B 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" C2' SAM C1302 " pdb=" C1' SAM C1302 " pdb=" C3' SAM C1302 " pdb=" O2' SAM C1302 " both_signs ideal model delta sigma weight residual False -2.76 -2.59 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TRP C 696 " pdb=" N TRP C 696 " pdb=" C TRP C 696 " pdb=" CB TRP C 696 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1647 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 217 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C LEU C 217 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU C 217 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR C 218 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR C 86 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 466 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C PHE C 466 " -0.022 2.00e-02 2.50e+03 pdb=" O PHE C 466 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU C 467 " 0.007 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 581 2.73 - 3.27: 10337 3.27 - 3.82: 17923 3.82 - 4.36: 22391 4.36 - 4.90: 36579 Nonbonded interactions: 87811 Sorted by model distance: nonbonded pdb=" OD2 ASP C 997 " pdb="MG MG C1301 " model vdw 2.190 2.170 nonbonded pdb=" OE1 GLU C1008 " pdb=" OG SER C1016 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C1054 " pdb=" OE1 GLU C1057 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP C 999 " pdb="MG MG C1301 " model vdw 2.266 2.170 nonbonded pdb=" O HIS C 318 " pdb=" OG1 THR C 321 " model vdw 2.302 3.040 ... (remaining 87806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.060 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 13.910 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 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 0.056 11119 Z= 0.242 Angle : 0.548 8.869 15252 Z= 0.375 Chirality : 0.041 0.183 1650 Planarity : 0.003 0.029 1801 Dihedral : 15.886 170.292 4279 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.29 % Allowed : 2.99 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1203 helix: 1.65 (0.23), residues: 578 sheet: -0.29 (0.66), residues: 67 loop : -0.61 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 744 TYR 0.023 0.001 TYR C 86 PHE 0.010 0.001 PHE C 537 TRP 0.011 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.24 (11119) covalent geometry : angle 0.54821 / 0.38 (15252) hydrogen bonds : bond 0.15677 / 11.18 ( 519) hydrogen bonds : angle 5.77107 / 4.14 ( 1419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.402 Fit side-chains REVERT: C 377 ARG cc_start: 0.8183 (tpp-160) cc_final: 0.7745 (tpp-160) REVERT: C 434 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7844 (mmtp) REVERT: C 437 MET cc_start: 0.7947 (mmm) cc_final: 0.7652 (mmm) REVERT: C 469 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7368 (mtt180) REVERT: C 479 ILE cc_start: 0.8505 (mm) cc_final: 0.7922 (mm) REVERT: C 517 MET cc_start: 0.9115 (mtp) cc_final: 0.8896 (mtm) REVERT: C 1148 ASP cc_start: 0.8109 (m-30) cc_final: 0.7805 (p0) outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.8394 time to fit residues: 82.7330 Evaluate side-chains 66 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 801 ASN C1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.063561 restraints weight = 17258.205| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.36 r_work: 0.2741 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11119 Z= 0.134 Angle : 0.550 8.522 15252 Z= 0.300 Chirality : 0.041 0.335 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.335 170.786 1903 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.64 % Allowed : 5.11 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.18 (0.25), residues: 1203 helix: 2.12 (0.22), residues: 580 sheet: 0.00 (0.61), residues: 77 loop : -0.57 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1165 TYR 0.023 0.001 TYR C 86 PHE 0.012 0.001 PHE C 537 TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (11119) covalent geometry : angle 0.55018 / 0.30 (15252) hydrogen bonds : bond 0.05774 / 4.10 ( 519) hydrogen bonds : angle 4.36054 / 3.14 ( 1419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 337 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7182 (ttp80) REVERT: C 394 LYS cc_start: 0.7887 (tppt) cc_final: 0.7301 (mmpt) REVERT: C 417 ASP cc_start: 0.5789 (p0) cc_final: 0.4839 (p0) REVERT: C 437 MET cc_start: 0.8245 (mmm) cc_final: 0.7987 (mmm) REVERT: C 472 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8216 (mtm110) REVERT: C 1148 ASP cc_start: 0.8149 (m-30) cc_final: 0.7832 (p0) outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 0.8565 time to fit residues: 71.7794 Evaluate side-chains 67 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 914 GLU Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062033 restraints weight = 17137.827| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.34 r_work: 0.2708 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11119 Z= 0.149 Angle : 0.570 9.435 15252 Z= 0.307 Chirality : 0.043 0.360 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.377 170.654 1903 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.06 % Allowed : 6.36 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1203 helix: 2.23 (0.22), residues: 579 sheet: 0.00 (0.61), residues: 79 loop : -0.65 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 339 TYR 0.022 0.001 TYR C 86 PHE 0.014 0.001 PHE C 537 TRP 0.010 0.001 TRP C 862 HIS 0.003 0.001 HIS C 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (11119) covalent geometry : angle 0.56976 / 0.31 (15252) hydrogen bonds : bond 0.05700 / 4.02 ( 519) hydrogen bonds : angle 4.08126 / 2.94 ( 1419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: C 4 ASN cc_start: 0.8135 (m-40) cc_final: 0.7926 (m-40) REVERT: C 394 LYS cc_start: 0.7937 (tppt) cc_final: 0.7446 (mmpt) REVERT: C 417 ASP cc_start: 0.6173 (p0) cc_final: 0.5383 (p0) REVERT: C 432 GLU cc_start: 0.7431 (pm20) cc_final: 0.6869 (pm20) REVERT: C 437 MET cc_start: 0.8288 (mmm) cc_final: 0.8027 (mmp) REVERT: C 472 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8278 (mtm110) REVERT: C 1148 ASP cc_start: 0.8188 (m-30) cc_final: 0.7878 (p0) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.9043 time to fit residues: 69.9511 Evaluate side-chains 72 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061698 restraints weight = 17282.790| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.34 r_work: 0.2703 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11119 Z= 0.152 Angle : 0.570 10.779 15252 Z= 0.306 Chirality : 0.043 0.360 1650 Planarity : 0.003 0.039 1801 Dihedral : 20.407 170.900 1903 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.35 % Allowed : 6.94 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1203 helix: 2.24 (0.22), residues: 578 sheet: 0.00 (0.61), residues: 79 loop : -0.69 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 377 TYR 0.021 0.001 TYR C 86 PHE 0.012 0.001 PHE C 537 TRP 0.010 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (11119) covalent geometry : angle 0.56950 / 0.31 (15252) hydrogen bonds : bond 0.05623 / 3.96 ( 519) hydrogen bonds : angle 4.01371 / 2.89 ( 1419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: C 4 ASN cc_start: 0.8153 (m-40) cc_final: 0.7934 (m-40) REVERT: C 394 LYS cc_start: 0.7940 (tppt) cc_final: 0.7520 (mmpt) REVERT: C 432 GLU cc_start: 0.7391 (pm20) cc_final: 0.6743 (pm20) REVERT: C 437 MET cc_start: 0.8277 (mmm) cc_final: 0.8033 (mmp) REVERT: C 469 ARG cc_start: 0.8506 (mtt180) cc_final: 0.8165 (ttt-90) REVERT: C 472 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8235 (mtm110) REVERT: C 638 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8635 (mmp) REVERT: C 1148 ASP cc_start: 0.8195 (m-30) cc_final: 0.7908 (p0) outliers start: 14 outliers final: 9 residues processed: 73 average time/residue: 0.8590 time to fit residues: 66.6661 Evaluate side-chains 74 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C1131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.060381 restraints weight = 17302.544| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.36 r_work: 0.2673 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11119 Z= 0.191 Angle : 0.605 11.763 15252 Z= 0.325 Chirality : 0.045 0.418 1650 Planarity : 0.003 0.040 1801 Dihedral : 20.475 172.335 1903 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.35 % Allowed : 7.32 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1203 helix: 2.16 (0.22), residues: 579 sheet: 0.01 (0.61), residues: 79 loop : -0.71 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.021 0.002 TYR C 86 PHE 0.013 0.002 PHE C 864 TRP 0.009 0.001 TRP C 862 HIS 0.004 0.001 HIS C 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (11119) covalent geometry : angle 0.60505 / 0.33 (15252) hydrogen bonds : bond 0.06281 / 4.40 ( 519) hydrogen bonds : angle 4.06992 / 2.93 ( 1419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.426 Fit side-chains REVERT: C 4 ASN cc_start: 0.8159 (m-40) cc_final: 0.7946 (m-40) REVERT: C 394 LYS cc_start: 0.7912 (tppt) cc_final: 0.7359 (mmpt) REVERT: C 432 GLU cc_start: 0.7337 (pm20) cc_final: 0.6712 (pm20) REVERT: C 437 MET cc_start: 0.8295 (mmm) cc_final: 0.8027 (mmp) REVERT: C 469 ARG cc_start: 0.8504 (mtt180) cc_final: 0.8244 (ttt-90) REVERT: C 472 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8253 (ttm110) REVERT: C 638 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8646 (mmp) REVERT: C 1148 ASP cc_start: 0.8207 (m-30) cc_final: 0.7930 (p0) outliers start: 14 outliers final: 8 residues processed: 71 average time/residue: 0.8778 time to fit residues: 66.1741 Evaluate side-chains 74 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 913 ILE Chi-restraints excluded: chain C residue 1109 MET Chi-restraints excluded: chain C residue 1147 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C 249 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.061791 restraints weight = 17276.568| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.35 r_work: 0.2703 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11119 Z= 0.133 Angle : 0.568 12.467 15252 Z= 0.303 Chirality : 0.042 0.357 1650 Planarity : 0.003 0.039 1801 Dihedral : 20.444 170.792 1903 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.06 % Allowed : 7.80 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1203 helix: 2.26 (0.22), residues: 579 sheet: 0.02 (0.62), residues: 79 loop : -0.71 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.020 0.001 TYR C 86 PHE 0.011 0.001 PHE C1021 TRP 0.010 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11119) covalent geometry : angle 0.56802 / 0.30 (15252) hydrogen bonds : bond 0.05323 / 3.75 ( 519) hydrogen bonds : angle 3.95178 / 2.85 ( 1419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: C 4 ASN cc_start: 0.8125 (m-40) cc_final: 0.7908 (m-40) REVERT: C 394 LYS cc_start: 0.7852 (tppt) cc_final: 0.7292 (mmpt) REVERT: C 432 GLU cc_start: 0.7219 (pm20) cc_final: 0.6473 (pm20) REVERT: C 437 MET cc_start: 0.8248 (mmm) cc_final: 0.7904 (mmt) REVERT: C 469 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8342 (ttt180) REVERT: C 472 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8186 (ttm110) REVERT: C 1148 ASP cc_start: 0.8197 (m-30) cc_final: 0.7917 (p0) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.8854 time to fit residues: 66.7149 Evaluate side-chains 70 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 1109 MET Chi-restraints excluded: chain C residue 1147 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 chunk 81 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 69 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C 610 ASN C1131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.063427 restraints weight = 17267.793| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.33 r_work: 0.2738 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11119 Z= 0.112 Angle : 0.533 11.589 15252 Z= 0.285 Chirality : 0.041 0.365 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.382 172.229 1903 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.35 % Allowed : 8.00 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1203 helix: 2.36 (0.22), residues: 578 sheet: 0.12 (0.62), residues: 79 loop : -0.68 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1127 TYR 0.021 0.001 TYR C 86 PHE 0.010 0.001 PHE C 864 TRP 0.010 0.001 TRP C 696 HIS 0.004 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11119) covalent geometry : angle 0.53335 / 0.29 (15252) hydrogen bonds : bond 0.04544 / 3.21 ( 519) hydrogen bonds : angle 3.80591 / 2.75 ( 1419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.399 Fit side-chains REVERT: C 146 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9106 (tm) REVERT: C 377 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7953 (tpp-160) REVERT: C 394 LYS cc_start: 0.7879 (tppt) cc_final: 0.7343 (mmpt) REVERT: C 432 GLU cc_start: 0.7146 (pm20) cc_final: 0.6906 (pm20) REVERT: C 472 ARG cc_start: 0.8555 (mtp85) cc_final: 0.8276 (ttm110) REVERT: C 638 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8637 (mmp) REVERT: C 1127 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7650 (ttm-80) REVERT: C 1148 ASP cc_start: 0.8179 (m-30) cc_final: 0.7913 (p0) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.7358 time to fit residues: 56.2262 Evaluate side-chains 71 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063219 restraints weight = 17270.599| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.35 r_work: 0.2736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11119 Z= 0.118 Angle : 0.560 13.679 15252 Z= 0.296 Chirality : 0.041 0.370 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.356 170.834 1903 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.77 % Allowed : 9.06 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1203 helix: 2.35 (0.22), residues: 580 sheet: 0.12 (0.62), residues: 79 loop : -0.66 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.021 0.001 TYR C 86 PHE 0.010 0.001 PHE C 537 TRP 0.008 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (11119) covalent geometry : angle 0.56017 / 0.30 (15252) hydrogen bonds : bond 0.04590 / 3.24 ( 519) hydrogen bonds : angle 3.79355 / 2.75 ( 1419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9124 (tm) REVERT: C 377 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7965 (tpp-160) REVERT: C 394 LYS cc_start: 0.7873 (tppt) cc_final: 0.7341 (mmpt) REVERT: C 432 GLU cc_start: 0.6875 (pm20) cc_final: 0.6456 (pm20) REVERT: C 437 MET cc_start: 0.7936 (mmm) cc_final: 0.7702 (mmm) REVERT: C 472 ARG cc_start: 0.8571 (mtp85) cc_final: 0.8270 (ttm110) REVERT: C 1127 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7662 (ttm-80) REVERT: C 1148 ASP cc_start: 0.8161 (m-30) cc_final: 0.7900 (p0) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.8788 time to fit residues: 64.3241 Evaluate side-chains 70 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN C 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.062936 restraints weight = 17215.942| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.34 r_work: 0.2730 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11119 Z= 0.122 Angle : 0.564 13.336 15252 Z= 0.298 Chirality : 0.041 0.370 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.353 170.341 1903 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.96 % Allowed : 8.86 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.25), residues: 1203 helix: 2.34 (0.22), residues: 580 sheet: 0.13 (0.62), residues: 79 loop : -0.66 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1127 TYR 0.021 0.001 TYR C 86 PHE 0.011 0.001 PHE C 537 TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11119) covalent geometry : angle 0.56379 / 0.30 (15252) hydrogen bonds : bond 0.04719 / 3.33 ( 519) hydrogen bonds : angle 3.80478 / 2.76 ( 1419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9132 (tm) REVERT: C 377 ARG cc_start: 0.8238 (tpp-160) cc_final: 0.7968 (tpp-160) REVERT: C 394 LYS cc_start: 0.7868 (tppt) cc_final: 0.7336 (mmpt) REVERT: C 432 GLU cc_start: 0.7027 (pm20) cc_final: 0.6440 (pm20) REVERT: C 437 MET cc_start: 0.7987 (mmm) cc_final: 0.7731 (mmm) REVERT: C 472 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8273 (ttm110) REVERT: C 1127 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7634 (ttm-80) REVERT: C 1148 ASP cc_start: 0.8154 (m-30) cc_final: 0.7905 (p0) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.7843 time to fit residues: 55.7364 Evaluate side-chains 71 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Chi-restraints excluded: chain C residue 1147 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 610 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.095059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062411 restraints weight = 17210.286| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.33 r_work: 0.2717 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11119 Z= 0.135 Angle : 0.588 13.809 15252 Z= 0.309 Chirality : 0.042 0.372 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.375 170.664 1903 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.87 % Allowed : 9.06 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1203 helix: 2.33 (0.22), residues: 579 sheet: 0.11 (0.62), residues: 79 loop : -0.68 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1127 TYR 0.021 0.001 TYR C 86 PHE 0.011 0.001 PHE C 537 TRP 0.008 0.001 TRP C 862 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11119) covalent geometry : angle 0.58810 / 0.31 (15252) hydrogen bonds : bond 0.04981 / 3.51 ( 519) hydrogen bonds : angle 3.82436 / 2.77 ( 1419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 146 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9100 (tm) REVERT: C 337 ARG cc_start: 0.7458 (mtp180) cc_final: 0.7255 (mtp180) REVERT: C 377 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7974 (tpp-160) REVERT: C 394 LYS cc_start: 0.7869 (tppt) cc_final: 0.7332 (mmpt) REVERT: C 418 MET cc_start: 0.5047 (mmm) cc_final: 0.4818 (mtp) REVERT: C 432 GLU cc_start: 0.7208 (pm20) cc_final: 0.6500 (pm20) REVERT: C 437 MET cc_start: 0.8018 (mmm) cc_final: 0.7814 (mmm) REVERT: C 472 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8260 (ttm110) REVERT: C 1148 ASP cc_start: 0.8149 (m-30) cc_final: 0.7912 (p0) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.8611 time to fit residues: 61.0790 Evaluate side-chains 68 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 406 PHE Chi-restraints excluded: chain C residue 684 ASP Chi-restraints excluded: chain C residue 826 THR Chi-restraints excluded: chain C residue 1109 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063520 restraints weight = 17308.718| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.33 r_work: 0.2743 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11119 Z= 0.114 Angle : 0.564 13.561 15252 Z= 0.296 Chirality : 0.041 0.366 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.345 171.344 1903 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.67 % Allowed : 9.15 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.25), residues: 1203 helix: 2.36 (0.22), residues: 579 sheet: 0.13 (0.62), residues: 79 loop : -0.66 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1127 TYR 0.021 0.001 TYR C 86 PHE 0.009 0.001 PHE C 782 TRP 0.009 0.001 TRP C 696 HIS 0.003 0.001 HIS C1166 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (11119) covalent geometry : angle 0.56407 / 0.30 (15252) hydrogen bonds : bond 0.04456 / 3.14 ( 519) hydrogen bonds : angle 3.75751 / 2.73 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5298.69 seconds wall clock time: 90 minutes 43.16 seconds (5443.16 seconds total)