Starting phenix.real_space_refine on Fri Jul 3 11:58:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.map" model { file = "/net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pft_71613/07_2026/9pft_71613.cif" } resolution = 3.07 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= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 74 5.16 5 C 8728 2.51 5 N 2328 2.21 5 O 2608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 13753 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 11260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1381, 11260 Classifications: {'peptide': 1381} Link IDs: {'PTRANS': 47, 'TRANS': 1333} Chain breaks: 4 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 430 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 470 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Chain: "E" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 839 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "P" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna3p': 3} Chain: "T" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 223 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 7} Time building chain proxies: 2.12, per 1000 atoms: 0.15 Number of scatterers: 13753 At special positions: 0 Unit cell: (102.473, 107.867, 126.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 15 15.00 O 2608 8.00 N 2328 7.00 C 8728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 417.1 milliseconds 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3184 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 9 sheets defined 63.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 4.093A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.864A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 334 removed outlier: 4.226A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 351 through 379 removed outlier: 4.198A pdb=" N PHE A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.816A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.583A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 553 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.561A pdb=" N MET A 558 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 596 through 604 Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 663 through 674 Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.593A pdb=" N ALA A 707 " --> pdb=" O PHE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 716 through 724 removed outlier: 3.837A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 900 through 920 removed outlier: 3.848A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.799A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.161A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 5.117A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 4.642A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1142 removed outlier: 3.843A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 3.603A pdb=" N GLU A1152 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1153' Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1366 through 1375 removed outlier: 4.253A pdb=" N ARG A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 3.801A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.656A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 156 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.975A pdb=" N GLY C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.802A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 200 removed outlier: 3.820A pdb=" N MET D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.222A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 631 Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 807 through 808 Processing sheet with id=AA7, first strand: chain 'A' and resid 874 through 875 removed outlier: 3.644A pdb=" N HIS A 875 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1228 through 1231 removed outlier: 3.590A pdb=" N ILE A1241 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1271 through 1272 762 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2232 1.31 - 1.43: 3643 1.43 - 1.56: 7995 1.56 - 1.69: 28 1.69 - 1.81: 125 Bond restraints: 14023 Sorted by residual: bond pdb=" C GLN A1062 " pdb=" O GLN A1062 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.32e-02 5.74e+03 1.78e+01 bond pdb=" C ASN A 448 " pdb=" O ASN A 448 " ideal model delta sigma weight residual 1.235 1.183 0.053 1.26e-02 6.30e+03 1.75e+01 bond pdb=" CG ASN A 448 " pdb=" ND2 ASN A 448 " ideal model delta sigma weight residual 1.328 1.252 0.076 2.10e-02 2.27e+03 1.31e+01 bond pdb=" CA GLN A1062 " pdb=" CB GLN A1062 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" CG GLN A1062 " pdb=" CD GLN A1062 " ideal model delta sigma weight residual 1.516 1.440 0.076 2.50e-02 1.60e+03 9.29e+00 ... (remaining 14018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 18684 2.29 - 4.59: 277 4.59 - 6.88: 39 6.88 - 9.18: 7 9.18 - 11.47: 5 Bond angle restraints: 19012 Sorted by residual: angle pdb=" CA CYS A 447 " pdb=" C CYS A 447 " pdb=" N ASN A 448 " ideal model delta sigma weight residual 117.93 124.11 -6.18 1.55e+00 4.16e-01 1.59e+01 angle pdb=" O CYS A 447 " pdb=" C CYS A 447 " pdb=" N ASN A 448 " ideal model delta sigma weight residual 122.20 116.40 5.80 1.46e+00 4.69e-01 1.58e+01 angle pdb=" C ASN A 448 " pdb=" CA ASN A 448 " pdb=" CB ASN A 448 " ideal model delta sigma weight residual 110.42 102.95 7.47 1.99e+00 2.53e-01 1.41e+01 angle pdb=" CA LEU A 499 " pdb=" CB LEU A 499 " pdb=" CG LEU A 499 " ideal model delta sigma weight residual 116.30 127.77 -11.47 3.50e+00 8.16e-02 1.07e+01 angle pdb=" C ASN A 448 " pdb=" N GLU A 449 " pdb=" CA GLU A 449 " ideal model delta sigma weight residual 123.00 127.49 -4.49 1.38e+00 5.25e-01 1.06e+01 ... (remaining 19007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.32: 8095 25.32 - 50.65: 434 50.65 - 75.97: 55 75.97 - 101.29: 7 101.29 - 126.62: 1 Dihedral angle restraints: 8592 sinusoidal: 3687 harmonic: 4905 Sorted by residual: dihedral pdb=" CA LEU A 499 " pdb=" C LEU A 499 " pdb=" N ASN A 500 " pdb=" CA ASN A 500 " ideal model delta harmonic sigma weight residual 180.00 -154.94 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLU A 349 " pdb=" C GLU A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA GLU A 825 " pdb=" C GLU A 825 " pdb=" N GLY A 826 " pdb=" CA GLY A 826 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 8589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1692 0.052 - 0.104: 432 0.104 - 0.157: 77 0.157 - 0.209: 15 0.209 - 0.261: 2 Chirality restraints: 2218 Sorted by residual: chirality pdb=" CA ASN A 448 " pdb=" N ASN A 448 " pdb=" C ASN A 448 " pdb=" CB ASN A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2215 not shown) Planarity restraints: 2338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 810 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C GLY A 810 " 0.053 2.00e-02 2.50e+03 pdb=" O GLY A 810 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 811 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 880 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 881 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 881 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 881 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 480 " 0.018 2.00e-02 2.50e+03 1.60e-02 6.39e+00 pdb=" CG TRP A 480 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 480 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 480 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 480 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 480 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 480 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 480 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 480 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 480 " 0.003 2.00e-02 2.50e+03 ... (remaining 2335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1341 2.74 - 3.28: 13798 3.28 - 3.82: 23555 3.82 - 4.36: 28750 4.36 - 4.90: 50041 Nonbonded interactions: 117485 Sorted by model distance: nonbonded pdb=" OH TYR A1126 " pdb=" OE1 GLU A1135 " model vdw 2.202 3.040 nonbonded pdb=" O ALA E 207 " pdb=" OG SER E 211 " model vdw 2.215 3.040 nonbonded pdb=" O ASN A 29 " pdb=" OG SER A 33 " model vdw 2.220 3.040 nonbonded pdb=" O SER A1223 " pdb=" OG1 THR A1227 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG A1357 " pdb=" OE1 GLU A1400 " model vdw 2.230 3.120 ... (remaining 117480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 183) selection = (chain 'C' and resid 130 through 183) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 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: 0.440 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.006 0.085 14023 Z= 0.253 Angle : 0.723 11.473 19012 Z= 0.379 Chirality : 0.048 0.261 2218 Planarity : 0.005 0.073 2338 Dihedral : 15.055 126.617 5408 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.06 % 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: 0.65 (0.20), residues: 1641 helix: 1.48 (0.16), residues: 960 sheet: -1.41 (0.50), residues: 89 loop : -0.99 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 511 TYR 0.024 0.002 TYR A 453 PHE 0.031 0.002 PHE A 868 TRP 0.042 0.002 TRP A 480 HIS 0.008 0.002 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (14023) covalent geometry : angle 0.72301 / 0.38 (19012) hydrogen bonds : bond 0.11360 / 7.73 ( 762) hydrogen bonds : angle 5.49173 / 3.93 ( 2205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 650 ASN cc_start: 0.8696 (m-40) cc_final: 0.8472 (m-40) REVERT: A 954 ASP cc_start: 0.8009 (m-30) cc_final: 0.7666 (m-30) REVERT: C 170 MET cc_start: 0.8030 (mmm) cc_final: 0.7594 (mmm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1150 time to fit residues: 35.9359 Evaluate side-chains 174 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 668 GLN E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136577 restraints weight = 15908.505| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.73 r_work: 0.3451 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14023 Z= 0.120 Angle : 0.524 7.997 19012 Z= 0.280 Chirality : 0.039 0.153 2218 Planarity : 0.004 0.047 2338 Dihedral : 9.197 126.934 2039 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.66 % Allowed : 6.38 % Favored : 92.97 % 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: 1.09 (0.21), residues: 1641 helix: 1.73 (0.16), residues: 976 sheet: -1.02 (0.53), residues: 89 loop : -0.72 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 511 TYR 0.017 0.001 TYR A 221 PHE 0.020 0.001 PHE A 868 TRP 0.014 0.001 TRP A 480 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14023) covalent geometry : angle 0.52352 / 0.28 (19012) hydrogen bonds : bond 0.03948 / 2.58 ( 762) hydrogen bonds : angle 4.62650 / 3.29 ( 2205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 864 ARG cc_start: 0.8123 (tmm-80) cc_final: 0.7818 (ptm160) REVERT: A 866 MET cc_start: 0.8688 (ttm) cc_final: 0.8439 (ttm) REVERT: A 918 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7975 (mtt90) REVERT: A 1034 ASP cc_start: 0.8261 (p0) cc_final: 0.7985 (p0) REVERT: A 1432 ASP cc_start: 0.7985 (t70) cc_final: 0.7704 (t70) REVERT: C 170 MET cc_start: 0.7730 (mmm) cc_final: 0.7295 (mmm) REVERT: C 177 MET cc_start: 0.7047 (mmm) cc_final: 0.6665 (mmm) outliers start: 10 outliers final: 8 residues processed: 205 average time/residue: 0.1148 time to fit residues: 34.1673 Evaluate side-chains 192 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 141 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136728 restraints weight = 15947.213| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.74 r_work: 0.3456 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14023 Z= 0.116 Angle : 0.483 8.068 19012 Z= 0.259 Chirality : 0.039 0.144 2218 Planarity : 0.004 0.047 2338 Dihedral : 9.000 125.740 2039 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.45 % Allowed : 8.09 % Favored : 90.47 % 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 (0.21), residues: 1641 helix: 1.92 (0.17), residues: 973 sheet: -0.85 (0.54), residues: 89 loop : -0.68 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 511 TYR 0.018 0.001 TYR A 221 PHE 0.019 0.001 PHE A 868 TRP 0.013 0.001 TRP A 480 HIS 0.004 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14023) covalent geometry : angle 0.48259 / 0.26 (19012) hydrogen bonds : bond 0.03730 / 2.43 ( 762) hydrogen bonds : angle 4.42227 / 3.14 ( 2205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 778 GLU cc_start: 0.8386 (tp30) cc_final: 0.8123 (mm-30) REVERT: A 866 MET cc_start: 0.8768 (ttm) cc_final: 0.8529 (ttm) REVERT: A 918 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7953 (mtt90) REVERT: A 1034 ASP cc_start: 0.8185 (p0) cc_final: 0.7868 (p0) REVERT: A 1432 ASP cc_start: 0.7989 (t0) cc_final: 0.7681 (t0) REVERT: C 170 MET cc_start: 0.7600 (mmm) cc_final: 0.7161 (mmm) REVERT: D 151 THR cc_start: 0.9151 (t) cc_final: 0.8785 (p) outliers start: 22 outliers final: 14 residues processed: 215 average time/residue: 0.1078 time to fit residues: 33.9525 Evaluate side-chains 196 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 640 GLN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 chunk 149 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133171 restraints weight = 15830.766| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.71 r_work: 0.3419 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14023 Z= 0.164 Angle : 0.512 8.379 19012 Z= 0.272 Chirality : 0.040 0.159 2218 Planarity : 0.004 0.048 2338 Dihedral : 8.967 125.811 2039 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.45 % Allowed : 9.80 % Favored : 88.76 % 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: 1.28 (0.21), residues: 1641 helix: 1.92 (0.17), residues: 972 sheet: -0.83 (0.52), residues: 89 loop : -0.70 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 511 TYR 0.021 0.001 TYR A1126 PHE 0.019 0.002 PHE A 424 TRP 0.013 0.002 TRP A 480 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 (14023) covalent geometry : angle 0.51156 / 0.27 (19012) hydrogen bonds : bond 0.03868 / 2.51 ( 762) hydrogen bonds : angle 4.41802 / 3.13 ( 2205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.323 Fit side-chains REVERT: A 497 TYR cc_start: 0.8738 (t80) cc_final: 0.8404 (t80) REVERT: A 918 ARG cc_start: 0.8213 (mtt180) cc_final: 0.8006 (mtt90) REVERT: A 1034 ASP cc_start: 0.8209 (p0) cc_final: 0.7868 (p0) REVERT: A 1432 ASP cc_start: 0.8011 (t0) cc_final: 0.7717 (t0) REVERT: C 170 MET cc_start: 0.7679 (mmm) cc_final: 0.7313 (mmm) REVERT: E 134 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6824 (mtp180) outliers start: 22 outliers final: 16 residues processed: 205 average time/residue: 0.1074 time to fit residues: 31.9695 Evaluate side-chains 195 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 154 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132195 restraints weight = 15959.807| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.74 r_work: 0.3371 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14023 Z= 0.191 Angle : 0.528 9.225 19012 Z= 0.279 Chirality : 0.041 0.156 2218 Planarity : 0.004 0.048 2338 Dihedral : 8.985 126.247 2039 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.58 % Allowed : 10.65 % Favored : 87.77 % 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 (0.21), residues: 1641 helix: 1.84 (0.17), residues: 973 sheet: -0.83 (0.52), residues: 89 loop : -0.74 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 511 TYR 0.023 0.002 TYR A1126 PHE 0.020 0.002 PHE A 424 TRP 0.013 0.002 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (14023) covalent geometry : angle 0.52760 / 0.28 (19012) hydrogen bonds : bond 0.04002 / 2.60 ( 762) hydrogen bonds : angle 4.40911 / 3.14 ( 2205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.388 Fit side-chains REVERT: A 918 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7982 (mtt90) REVERT: A 1034 ASP cc_start: 0.8213 (p0) cc_final: 0.7846 (p0) REVERT: A 1173 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8576 (mt) REVERT: A 1228 MET cc_start: 0.8739 (mmt) cc_final: 0.8117 (mmt) REVERT: A 1273 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7758 (mmt) REVERT: A 1339 ARG cc_start: 0.8497 (mtt90) cc_final: 0.8291 (mtt90) REVERT: A 1432 ASP cc_start: 0.8013 (t0) cc_final: 0.7730 (t0) REVERT: C 170 MET cc_start: 0.7636 (mmm) cc_final: 0.7273 (mmm) REVERT: E 134 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6854 (mtp180) outliers start: 24 outliers final: 17 residues processed: 204 average time/residue: 0.1014 time to fit residues: 30.5701 Evaluate side-chains 196 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 126 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135510 restraints weight = 15667.577| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.71 r_work: 0.3449 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14023 Z= 0.105 Angle : 0.465 9.627 19012 Z= 0.249 Chirality : 0.038 0.179 2218 Planarity : 0.003 0.045 2338 Dihedral : 8.862 125.221 2039 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.64 % Allowed : 11.57 % Favored : 86.79 % 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: 1.42 (0.21), residues: 1641 helix: 2.03 (0.17), residues: 972 sheet: -0.61 (0.54), residues: 89 loop : -0.68 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.016 0.001 TYR A 221 PHE 0.012 0.001 PHE A 629 TRP 0.014 0.001 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14023) covalent geometry : angle 0.46497 / 0.25 (19012) hydrogen bonds : bond 0.03490 / 2.27 ( 762) hydrogen bonds : angle 4.23370 / 3.02 ( 2205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.373 Fit side-chains REVERT: A 918 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7886 (mtt90) REVERT: A 1034 ASP cc_start: 0.8173 (p0) cc_final: 0.7803 (p0) REVERT: A 1173 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8590 (mt) REVERT: A 1228 MET cc_start: 0.8668 (mmt) cc_final: 0.8169 (mmt) REVERT: A 1273 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7665 (mmt) REVERT: A 1339 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8231 (mtt90) REVERT: A 1432 ASP cc_start: 0.8173 (t0) cc_final: 0.7876 (t0) REVERT: C 170 MET cc_start: 0.7675 (mmm) cc_final: 0.7303 (mmm) REVERT: C 177 MET cc_start: 0.7124 (mmm) cc_final: 0.6495 (mmm) outliers start: 25 outliers final: 18 residues processed: 206 average time/residue: 0.0955 time to fit residues: 29.4745 Evaluate side-chains 200 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119303 restraints weight = 16312.119| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.76 r_work: 0.3245 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 14023 Z= 0.234 Angle : 0.573 10.387 19012 Z= 0.301 Chirality : 0.043 0.192 2218 Planarity : 0.004 0.046 2338 Dihedral : 8.960 125.858 2039 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.84 % Allowed : 11.70 % Favored : 86.46 % 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 (0.21), residues: 1641 helix: 1.80 (0.17), residues: 972 sheet: -0.58 (0.53), residues: 89 loop : -0.73 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 511 TYR 0.024 0.002 TYR A1126 PHE 0.024 0.002 PHE A 424 TRP 0.013 0.002 TRP A 732 HIS 0.007 0.002 HIS A 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.23 (14023) covalent geometry : angle 0.57315 / 0.30 (19012) hydrogen bonds : bond 0.04198 / 2.72 ( 762) hydrogen bonds : angle 4.42844 / 3.15 ( 2205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.387 Fit side-chains REVERT: A 918 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7902 (mtt90) REVERT: A 1034 ASP cc_start: 0.8081 (p0) cc_final: 0.7761 (p0) REVERT: A 1173 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8581 (mt) REVERT: A 1228 MET cc_start: 0.8664 (mmt) cc_final: 0.8073 (mmt) REVERT: A 1273 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7718 (mmt) REVERT: A 1339 ARG cc_start: 0.8397 (mtt90) cc_final: 0.8130 (mtt90) REVERT: A 1422 MET cc_start: 0.8891 (ttp) cc_final: 0.8500 (ttp) REVERT: A 1432 ASP cc_start: 0.8175 (t0) cc_final: 0.7821 (t0) outliers start: 28 outliers final: 22 residues processed: 200 average time/residue: 0.1054 time to fit residues: 30.9297 Evaluate side-chains 199 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1406 CYS Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 141 LYS Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126964 restraints weight = 16090.114| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.86 r_work: 0.3330 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14023 Z= 0.112 Angle : 0.476 9.559 19012 Z= 0.255 Chirality : 0.038 0.182 2218 Planarity : 0.004 0.044 2338 Dihedral : 8.859 125.163 2039 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.71 % Allowed : 12.36 % Favored : 85.93 % 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 (0.21), residues: 1641 helix: 1.98 (0.17), residues: 971 sheet: -0.59 (0.53), residues: 89 loop : -0.70 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.017 0.001 TYR A1126 PHE 0.022 0.001 PHE A 868 TRP 0.015 0.001 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (14023) covalent geometry : angle 0.47614 / 0.26 (19012) hydrogen bonds : bond 0.03585 / 2.32 ( 762) hydrogen bonds : angle 4.25290 / 3.04 ( 2205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.412 Fit side-chains REVERT: A 918 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7721 (mtt90) REVERT: A 1034 ASP cc_start: 0.7980 (p0) cc_final: 0.7666 (p0) REVERT: A 1173 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8530 (mt) REVERT: A 1228 MET cc_start: 0.8589 (mmt) cc_final: 0.8031 (mmt) REVERT: A 1273 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7753 (mmt) REVERT: A 1419 ILE cc_start: 0.7986 (mm) cc_final: 0.7710 (mm) REVERT: A 1422 MET cc_start: 0.8914 (ttp) cc_final: 0.8538 (ttp) REVERT: A 1432 ASP cc_start: 0.8132 (t0) cc_final: 0.7767 (t0) REVERT: C 177 MET cc_start: 0.7017 (mmm) cc_final: 0.6528 (mmm) REVERT: E 134 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6446 (ptp90) outliers start: 26 outliers final: 19 residues processed: 203 average time/residue: 0.0990 time to fit residues: 29.8026 Evaluate side-chains 201 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 104 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126436 restraints weight = 16241.923| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.87 r_work: 0.3277 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 0.049 14023 Z= 0.128 Angle : 0.495 9.569 19012 Z= 0.262 Chirality : 0.039 0.193 2218 Planarity : 0.004 0.044 2338 Dihedral : 8.809 124.238 2039 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.45 % Allowed : 13.41 % Favored : 85.14 % 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: 1.38 (0.21), residues: 1641 helix: 1.99 (0.17), residues: 973 sheet: -0.55 (0.53), residues: 89 loop : -0.70 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 511 TYR 0.020 0.001 TYR A1126 PHE 0.016 0.001 PHE A 629 TRP 0.014 0.001 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14023) covalent geometry : angle 0.49494 / 0.26 (19012) hydrogen bonds : bond 0.03627 / 2.35 ( 762) hydrogen bonds : angle 4.25162 / 3.04 ( 2205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.503 Fit side-chains REVERT: A 774 MET cc_start: 0.7744 (mmt) cc_final: 0.7351 (mmt) REVERT: A 918 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7762 (mtt90) REVERT: A 1034 ASP cc_start: 0.8016 (p0) cc_final: 0.7700 (p0) REVERT: A 1173 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8601 (mt) REVERT: A 1226 TYR cc_start: 0.8633 (t80) cc_final: 0.8339 (t80) REVERT: A 1228 MET cc_start: 0.8634 (mmt) cc_final: 0.8108 (mmt) REVERT: A 1273 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7685 (mmt) REVERT: A 1419 ILE cc_start: 0.8065 (mm) cc_final: 0.7790 (mm) REVERT: A 1422 MET cc_start: 0.8914 (ttp) cc_final: 0.8548 (ttp) REVERT: A 1432 ASP cc_start: 0.8135 (t0) cc_final: 0.7793 (t0) REVERT: C 177 MET cc_start: 0.7109 (mmm) cc_final: 0.6568 (mmm) outliers start: 22 outliers final: 19 residues processed: 201 average time/residue: 0.0990 time to fit residues: 29.7906 Evaluate side-chains 201 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 153 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 136 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126926 restraints weight = 16111.665| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.82 r_work: 0.3314 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14023 Z= 0.107 Angle : 0.470 9.275 19012 Z= 0.252 Chirality : 0.038 0.199 2218 Planarity : 0.003 0.045 2338 Dihedral : 8.705 123.138 2039 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.64 % Allowed : 13.48 % Favored : 84.88 % 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: 1.44 (0.21), residues: 1641 helix: 2.05 (0.17), residues: 973 sheet: -0.53 (0.54), residues: 89 loop : -0.69 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 511 TYR 0.018 0.001 TYR A1126 PHE 0.013 0.001 PHE A 629 TRP 0.015 0.001 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14023) covalent geometry : angle 0.46968 / 0.25 (19012) hydrogen bonds : bond 0.03462 / 2.24 ( 762) hydrogen bonds : angle 4.19829 / 3.00 ( 2205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3282 Ramachandran restraints generated. 1641 Oldfield, 0 Emsley, 1641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.383 Fit side-chains REVERT: A 918 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7723 (mtt90) REVERT: A 1034 ASP cc_start: 0.8018 (p0) cc_final: 0.7666 (p0) REVERT: A 1173 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 1228 MET cc_start: 0.8624 (mmt) cc_final: 0.8112 (mmt) REVERT: A 1273 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7682 (mmt) REVERT: A 1339 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8196 (mtt90) REVERT: A 1422 MET cc_start: 0.8959 (ttp) cc_final: 0.8608 (ttp) REVERT: A 1432 ASP cc_start: 0.8126 (t0) cc_final: 0.7775 (t0) REVERT: C 177 MET cc_start: 0.7106 (mmm) cc_final: 0.6550 (mmm) outliers start: 25 outliers final: 21 residues processed: 204 average time/residue: 0.0953 time to fit residues: 29.4343 Evaluate side-chains 203 residues out of total 1521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 831 GLN Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain A residue 942 LYS Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1273 MET Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain E residue 141 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 119 optimal weight: 7.9990 chunk 122 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 138 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.153398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124264 restraints weight = 16200.467| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.88 r_work: 0.3257 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14023 Z= 0.170 Angle : 0.517 9.824 19012 Z= 0.275 Chirality : 0.041 0.205 2218 Planarity : 0.004 0.046 2338 Dihedral : 8.719 122.921 2039 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.51 % Allowed : 13.87 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.21), residues: 1641 helix: 1.93 (0.17), residues: 972 sheet: -0.50 (0.54), residues: 89 loop : -0.69 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 511 TYR 0.023 0.001 TYR A1126 PHE 0.021 0.002 PHE A 629 TRP 0.013 0.001 TRP A 932 HIS 0.005 0.001 HIS A1338 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (14023) covalent geometry : angle 0.51743 / 0.28 (19012) hydrogen bonds : bond 0.03818 / 2.47 ( 762) hydrogen bonds : angle 4.28933 / 3.06 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.77 seconds wall clock time: 47 minutes 19.95 seconds (2839.95 seconds total)