Starting phenix.real_space_refine on Thu Jul 2 23:19:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewz_50027/07_2026/9ewz_50027.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewz_50027/07_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_50027/07_2026/9ewz_50027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewz_50027/07_2026/9ewz_50027.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewz_50027/07_2026/9ewz_50027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewz_50027/07_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-dev-6108/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: 2.68, per 1000 atoms: 0.25 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: 1.95 Conformation dependent library (CDL) restraints added in 364.2 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: 1.41 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: 2.60 Time building geometry restraints manager: 1.34 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: 14964 1.77 - 3.55: 255 3.55 - 5.32: 25 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: 8.820 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 : 0.546 8.869 15252 Z= 0.372 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 0.54626 / 0.37 (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 : 0.448 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: 0.8341 time to fit residues: 82.1245 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 : 0.435 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.063890 restraints weight = 17216.792| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.49 r_work: 0.2734 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0796 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= 0.131 Angle : 0.548 8.710 15252 Z= 0.299 Chirality : 0.041 0.315 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.366 171.562 1903 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.64 % Allowed : 5.30 % Favored : 93.06 % 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: 2.13 (0.22), residues: 580 sheet: -0.01 (0.61), residues: 77 loop : -0.58 (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 0.013 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 0.00267 / 0.13 (11119) covalent geometry : angle 0.54808 / 0.30 (15252) hydrogen bonds : bond 0.05588 / 3.96 ( 519) hydrogen bonds : angle 4.30063 / 3.10 ( 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 86 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: C 337 ARG cc_start: 0.7468 (mtp180) cc_final: 0.7162 (ttp80) REVERT: C 394 LYS cc_start: 0.7892 (tppt) cc_final: 0.7306 (mmpt) REVERT: C 417 ASP cc_start: 0.5767 (p0) cc_final: 0.4829 (p0) REVERT: C 437 MET cc_start: 0.8230 (mmm) cc_final: 0.7971 (mmm) REVERT: C 472 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8199 (mtm110) REVERT: C 1148 ASP cc_start: 0.8155 (m-30) cc_final: 0.7839 (p0) outliers start: 17 outliers final: 6 residues processed: 80 average time/residue: 0.7569 time to fit residues: 64.2935 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 143 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 91 optimal weight: 0.0470 chunk 93 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.6882 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.095811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.063459 restraints weight = 17154.085| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.34 r_work: 0.2739 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0976 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= 0.123 Angle : 0.534 8.954 15252 Z= 0.289 Chirality : 0.041 0.325 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.363 170.890 1903 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.96 % Allowed : 6.17 % Favored : 92.87 % 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: 1.27 (0.25), residues: 1203 helix: 2.28 (0.22), residues: 579 sheet: 0.01 (0.61), residues: 79 loop : -0.63 (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 0.012 0.001 PHE C 537 TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (11119) covalent geometry : angle 0.53378 / 0.29 (15252) hydrogen bonds : bond 0.05076 / 3.59 ( 519) hydrogen bonds : angle 4.01939 / 2.90 ( 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 76 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: C 394 LYS cc_start: 0.7920 (tppt) cc_final: 0.7426 (mmpt) REVERT: C 417 ASP cc_start: 0.6152 (p0) cc_final: 0.5401 (p0) REVERT: C 432 GLU cc_start: 0.7466 (pm20) cc_final: 0.6593 (pm20) REVERT: C 437 MET cc_start: 0.8269 (mmm) cc_final: 0.7855 (mmm) REVERT: C 469 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8112 (mtt180) REVERT: C 472 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8185 (mtm110) REVERT: C 1148 ASP cc_start: 0.8166 (m-30) cc_final: 0.7852 (p0) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.8127 time to fit residues: 60.2779 Evaluate side-chains 69 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 74 optimal weight: 0.0050 chunk 121 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.096548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.063829 restraints weight = 17364.624| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.37 r_work: 0.2742 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1093 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= 0.116 Angle : 0.531 11.242 15252 Z= 0.285 Chirality : 0.040 0.328 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.351 171.561 1903 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.06 % Allowed : 7.51 % Favored : 91.43 % 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: 2.33 (0.22), residues: 579 sheet: 0.03 (0.61), residues: 79 loop : -0.62 (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 0.011 0.001 PHE C 537 TRP 0.009 0.001 TRP C 862 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (11119) covalent geometry : angle 0.53103 / 0.28 (15252) hydrogen bonds : bond 0.04758 / 3.36 ( 519) hydrogen bonds : angle 3.88530 / 2.81 ( 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 78 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 394 LYS cc_start: 0.7898 (tppt) cc_final: 0.7407 (mmpt) REVERT: C 432 GLU cc_start: 0.7372 (pm20) cc_final: 0.6352 (pm20) REVERT: C 437 MET cc_start: 0.8290 (mmm) cc_final: 0.7900 (mmt) REVERT: C 472 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8262 (mtm110) REVERT: C 1148 ASP cc_start: 0.8159 (m-30) cc_final: 0.7876 (p0) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.8076 time to fit residues: 61.0168 Evaluate side-chains 72 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 1147 ARG 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: 0.8980 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN 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 = 0.095279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.062470 restraints weight = 17297.230| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.35 r_work: 0.2717 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.141 Angle : 0.551 11.660 15252 Z= 0.296 Chirality : 0.042 0.335 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.371 171.676 1903 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.35 % Allowed : 7.71 % Favored : 90.94 % 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: 1.30 (0.25), residues: 1203 helix: 2.32 (0.22), residues: 579 sheet: 0.05 (0.61), residues: 79 loop : -0.64 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 469 TYR 0.022 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 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11119) covalent geometry : angle 0.55112 / 0.30 (15252) hydrogen bonds : bond 0.05246 / 3.69 ( 519) hydrogen bonds : angle 3.90948 / 2.82 ( 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 : 0.283 Fit side-chains revert: symmetry clash REVERT: C 394 LYS cc_start: 0.7833 (tppt) cc_final: 0.7294 (mmpt) REVERT: C 432 GLU cc_start: 0.7378 (pm20) cc_final: 0.6345 (pm20) REVERT: C 437 MET cc_start: 0.8264 (mmm) cc_final: 0.7893 (mmt) REVERT: C 638 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8640 (mmp) REVERT: C 1148 ASP cc_start: 0.8175 (m-30) cc_final: 0.7888 (p0) outliers start: 14 outliers final: 8 residues processed: 71 average time/residue: 0.7745 time to fit residues: 58.3032 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 : 0.414 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.0470 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.064396 restraints weight = 17322.305| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.35 r_work: 0.2756 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11119 Z= 0.107 Angle : 0.526 12.666 15252 Z= 0.281 Chirality : 0.040 0.325 1650 Planarity : 0.003 0.037 1801 Dihedral : 20.328 172.921 1903 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.06 % Allowed : 8.29 % 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: 1.36 (0.25), residues: 1203 helix: 2.40 (0.22), residues: 580 sheet: -0.19 (0.65), residues: 67 loop : -0.60 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1127 TYR 0.020 0.001 TYR C 86 PHE 0.009 0.001 PHE C 782 TRP 0.009 0.001 TRP C 862 HIS 0.006 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (11119) covalent geometry : angle 0.52619 / 0.28 (15252) hydrogen bonds : bond 0.04404 / 3.11 ( 519) hydrogen bonds : angle 3.77888 / 2.73 ( 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 78 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 377 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.8148 (tpp-160) REVERT: C 394 LYS cc_start: 0.7805 (tppt) cc_final: 0.7259 (mmpt) REVERT: C 432 GLU cc_start: 0.7241 (pm20) cc_final: 0.6205 (pm20) REVERT: C 437 MET cc_start: 0.8274 (mmm) cc_final: 0.7889 (mmt) REVERT: C 1148 ASP cc_start: 0.8160 (m-30) cc_final: 0.7884 (p0) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.7775 time to fit residues: 57.6702 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 : 0.410 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.0170 chunk 81 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.061869 restraints weight = 17205.235| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.35 r_work: 0.2703 rms_B_bonded: 2.90 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: 0.8961 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11119 Z= 0.150 Angle : 0.572 12.641 15252 Z= 0.307 Chirality : 0.043 0.347 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.374 172.350 1903 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.06 % Allowed : 8.38 % Favored : 90.56 % 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: 1.30 (0.25), residues: 1203 helix: 2.34 (0.22), residues: 579 sheet: 0.09 (0.61), residues: 79 loop : -0.67 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 472 TYR 0.022 0.001 TYR C 86 PHE 0.013 0.001 PHE C 537 TRP 0.008 0.001 TRP C 862 HIS 0.004 0.001 HIS C 976 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11119) covalent geometry : angle 0.57193 / 0.31 (15252) hydrogen bonds : bond 0.05443 / 3.83 ( 519) hydrogen bonds : angle 3.87258 / 2.80 ( 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 76 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: C 394 LYS cc_start: 0.7837 (tppt) cc_final: 0.7295 (mmpt) REVERT: C 432 GLU cc_start: 0.7255 (pm20) cc_final: 0.6899 (pm20) REVERT: C 472 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8298 (ttm110) REVERT: C 638 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8676 (mmp) REVERT: C 1148 ASP cc_start: 0.8165 (m-30) cc_final: 0.7903 (p0) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.7396 time to fit residues: 53.9021 Evaluate side-chains 69 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 684 ASP 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: 5.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.062618 restraints weight = 17231.696| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.35 r_work: 0.2722 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11119 Z= 0.130 Angle : 0.568 12.395 15252 Z= 0.301 Chirality : 0.041 0.333 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.355 171.300 1903 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.77 % Allowed : 8.96 % Favored : 90.27 % 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: 580 sheet: 0.05 (0.61), residues: 79 loop : -0.67 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 412 TYR 0.020 0.001 TYR C 86 PHE 0.011 0.001 PHE C 537 TRP 0.009 0.001 TRP C 862 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11119) covalent geometry : angle 0.56768 / 0.30 (15252) hydrogen bonds : bond 0.04972 / 3.51 ( 519) hydrogen bonds : angle 3.83114 / 2.77 ( 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 72 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.404 Fit side-chains REVERT: C 377 ARG cc_start: 0.8314 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: C 394 LYS cc_start: 0.7824 (tppt) cc_final: 0.7273 (mmpt) REVERT: C 432 GLU cc_start: 0.6980 (pm20) cc_final: 0.6503 (pm20) REVERT: C 437 MET cc_start: 0.8000 (mmm) cc_final: 0.7718 (mmm) REVERT: C 472 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8200 (ttm110) REVERT: C 638 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8644 (mmp) REVERT: C 1148 ASP cc_start: 0.8164 (m-30) cc_final: 0.7906 (p0) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 0.8071 time to fit residues: 57.3697 Evaluate side-chains 68 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 1109 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 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: 0.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.061151 restraints weight = 17191.283| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.35 r_work: 0.2690 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11119 Z= 0.169 Angle : 0.609 13.383 15252 Z= 0.322 Chirality : 0.044 0.367 1650 Planarity : 0.003 0.039 1801 Dihedral : 20.398 172.742 1903 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.96 % Allowed : 8.77 % Favored : 90.27 % 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: 2.25 (0.22), residues: 580 sheet: 0.03 (0.61), residues: 79 loop : -0.68 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 339 TYR 0.021 0.001 TYR C 86 PHE 0.014 0.002 PHE C 537 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 0.00388 / 0.17 (11119) covalent geometry : angle 0.60945 / 0.32 (15252) hydrogen bonds : bond 0.05733 / 4.03 ( 519) hydrogen bonds : angle 3.92002 / 2.84 ( 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 73 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.353 Fit side-chains REVERT: C 4 ASN cc_start: 0.8119 (m-40) cc_final: 0.7889 (m-40) REVERT: C 394 LYS cc_start: 0.7841 (tppt) cc_final: 0.7288 (mmpt) REVERT: C 432 GLU cc_start: 0.7050 (pm20) cc_final: 0.6595 (pm20) REVERT: C 437 MET cc_start: 0.8005 (mmm) cc_final: 0.7748 (mmm) REVERT: C 472 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8238 (ttm110) REVERT: C 638 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8662 (mmp) REVERT: C 1148 ASP cc_start: 0.8186 (m-30) cc_final: 0.7937 (p0) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.8073 time to fit residues: 56.5015 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 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 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: 0.3980 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.095659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.063094 restraints weight = 17186.713| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.34 r_work: 0.2732 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1405 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= 0.115 Angle : 0.573 13.868 15252 Z= 0.300 Chirality : 0.041 0.331 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.330 170.758 1901 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.30 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: 1.27 (0.25), residues: 1203 helix: 2.34 (0.22), residues: 580 sheet: -0.18 (0.66), residues: 67 loop : -0.66 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 377 TYR 0.020 0.001 TYR C 86 PHE 0.019 0.001 PHE C 406 TRP 0.010 0.001 TRP C 696 HIS 0.007 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11119) covalent geometry : angle 0.57264 / 0.30 (15252) hydrogen bonds : bond 0.04697 / 3.31 ( 519) hydrogen bonds : angle 3.81648 / 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 73 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.444 Fit side-chains REVERT: C 394 LYS cc_start: 0.7862 (tppt) cc_final: 0.7314 (mmpt) REVERT: C 432 GLU cc_start: 0.7137 (pm20) cc_final: 0.6473 (pm20) REVERT: C 437 MET cc_start: 0.8115 (mmm) cc_final: 0.7691 (mmm) REVERT: C 472 ARG cc_start: 0.8569 (mtm110) cc_final: 0.8263 (ttm110) REVERT: C 1148 ASP cc_start: 0.8149 (m-30) cc_final: 0.7917 (p0) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.8318 time to fit residues: 60.9557 Evaluate side-chains 68 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 0.0370 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061583 restraints weight = 17236.519| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.32 r_work: 0.2701 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11119 Z= 0.157 Angle : 0.606 13.369 15252 Z= 0.320 Chirality : 0.043 0.351 1650 Planarity : 0.003 0.038 1801 Dihedral : 20.364 172.406 1901 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: 1.23 (0.25), residues: 1203 helix: 2.26 (0.22), residues: 580 sheet: 0.07 (0.61), residues: 79 loop : -0.68 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 469 TYR 0.021 0.001 TYR C 86 PHE 0.013 0.001 PHE C 537 TRP 0.009 0.001 TRP C 401 HIS 0.004 0.001 HIS C 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (11119) covalent geometry : angle 0.60648 / 0.32 (15252) hydrogen bonds : bond 0.05464 / 3.85 ( 519) hydrogen bonds : angle 3.89571 / 2.82 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4869.40 seconds wall clock time: 83 minutes 23.26 seconds (5003.26 seconds total)