Starting phenix.real_space_refine on Sat Jul 4 16:12:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144.map" model { file = "/net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p05_13144/07_2026/7p05_13144_trim.cif" } resolution = 3.13 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= 0.001 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 5 5.49 5 S 68 5.16 5 C 7050 2.51 5 N 1796 2.21 5 O 1982 1.98 5 H 10675 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 21576 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 21485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 21485 Classifications: {'peptide': 1353} Link IDs: {'PTRANS': 52, 'TRANS': 1300} Chain breaks: 5 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 91 Unusual residues: {'ADP': 1, 'ATP': 1, 'RHQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.11, per 1000 atoms: 0.14 Number of scatterers: 21576 At special positions: 0 Unit cell: (104.32, 95.844, 148.656, 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 68 16.00 P 5 15.00 O 1982 8.00 N 1796 7.00 C 7050 6.00 H 10675 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1411 " - pdb=" SG CYS A1455 " distance=2.04 Simple disulfide: pdb=" SG CYS A1427 " - pdb=" SG CYS A1452 " distance=2.02 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: 1.69 Conformation dependent library (CDL) restraints added in 556.4 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 7 sheets defined 63.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 36 through 56 Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.659A pdb=" N ALA A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 165 Processing helix chain 'A' and resid 198 through 207 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.820A pdb=" N VAL A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 291 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 310 through 326 Processing helix chain 'A' and resid 340 through 359 Processing helix chain 'A' and resid 370 through 375 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.573A pdb=" N GLN A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 519 Processing helix chain 'A' and resid 519 through 548 removed outlier: 3.771A pdb=" N THR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 548 " --> pdb=" O ILE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 569 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 591 Proline residue: A 583 - end of helix removed outlier: 3.651A pdb=" N TYR A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.520A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 626 removed outlier: 3.653A pdb=" N PHE A 624 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 659 removed outlier: 3.536A pdb=" N LEU A 659 " --> pdb=" O CYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 4.559A pdb=" N VAL A 668 " --> pdb=" O SER A 664 " (cutoff:3.500A) Proline residue: A 669 - end of helix Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.825A pdb=" N TRP A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.560A pdb=" N TYR A 705 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 736 through 740 Processing helix chain 'A' and resid 756 through 764 Processing helix chain 'A' and resid 767 through 771 Processing helix chain 'A' and resid 772 through 796 Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 941 through 946 Processing helix chain 'A' and resid 960 through 973 Processing helix chain 'A' and resid 978 through 994 Processing helix chain 'A' and resid 995 through 999 removed outlier: 3.648A pdb=" N ALA A 999 " --> pdb=" O GLU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1025 removed outlier: 3.511A pdb=" N GLU A1023 " --> pdb=" O THR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1060 Processing helix chain 'A' and resid 1071 through 1076 removed outlier: 3.695A pdb=" N GLN A1076 " --> pdb=" O ALA A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1100 through 1110 removed outlier: 3.509A pdb=" N HIS A1110 " --> pdb=" O TYR A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'A' and resid 1148 through 1164 removed outlier: 3.554A pdb=" N ARG A1152 " --> pdb=" O SER A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1200 Processing helix chain 'A' and resid 1202 through 1224 Processing helix chain 'A' and resid 1230 through 1246 removed outlier: 3.658A pdb=" N GLN A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1270 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1305 Proline residue: A1291 - end of helix Processing helix chain 'A' and resid 1309 through 1317 Processing helix chain 'A' and resid 1319 through 1347 Processing helix chain 'A' and resid 1351 through 1369 removed outlier: 3.518A pdb=" N ALA A1355 " --> pdb=" O VAL A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1379 Processing helix chain 'A' and resid 1380 through 1382 No H-bonds generated for 'chain 'A' and resid 1380 through 1382' Processing helix chain 'A' and resid 1383 through 1390 Processing helix chain 'A' and resid 1390 through 1405 removed outlier: 4.268A pdb=" N TYR A1394 " --> pdb=" O SER A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1416 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1431 through 1438 removed outlier: 3.638A pdb=" N LEU A1437 " --> pdb=" O PRO A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1468 removed outlier: 3.658A pdb=" N TYR A1463 " --> pdb=" O THR A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1500 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 182 removed outlier: 6.373A pdb=" N ALA A 136 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS A 177 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU A 134 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A 179 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 132 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 181 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 130 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 182 removed outlier: 6.373A pdb=" N ALA A 136 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS A 177 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU A 134 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N MET A 179 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 132 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 181 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 130 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.347A pdb=" N LEU A 189 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 380 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 391 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 382 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 719 through 721 Processing sheet with id=AA5, first strand: chain 'A' and resid 885 through 895 removed outlier: 6.705A pdb=" N ILE A 887 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU A 877 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN A 889 " --> pdb=" O CYS A 875 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS A 875 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL A 891 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 874 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 928 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR A 876 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 926 " --> pdb=" O TYR A 876 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 947 through 949 removed outlier: 6.311A pdb=" N GLY A 947 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ASP A1035 " --> pdb=" O GLY A 947 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N CYS A 949 " --> pdb=" O ASP A1035 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A1081 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A1093 " --> pdb=" O LEU A1081 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A1083 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1417 through 1419 629 hydrogen bonds defined for protein. 1809 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: 5.31 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10653 1.04 - 1.23: 669 1.23 - 1.43: 4286 1.43 - 1.63: 6144 1.63 - 1.83: 108 Bond restraints: 21860 Sorted by residual: bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" C11 RHQ A1603 " pdb=" N1 RHQ A1603 " ideal model delta sigma weight residual 1.437 1.335 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C5 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.387 1.338 0.049 1.00e-02 1.00e+04 2.41e+01 bond pdb=" C4 ATP A1601 " pdb=" N9 ATP A1601 " ideal model delta sigma weight residual 1.374 1.328 0.046 1.00e-02 1.00e+04 2.12e+01 ... (remaining 21855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 39313 7.09 - 14.17: 7 14.17 - 21.26: 2 21.26 - 28.35: 0 28.35 - 35.43: 6 Bond angle restraints: 39328 Sorted by residual: angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 119.75 20.12 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 120.62 16.21 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 109.00 73.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 109.00 74.08 34.92 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ASP A 120 " pdb=" CA ASP A 120 " pdb=" HA ASP A 120 " ideal model delta sigma weight residual 110.00 75.34 34.66 3.00e+00 1.11e-01 1.34e+02 ... (remaining 39323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 9758 21.63 - 43.26: 475 43.26 - 64.89: 127 64.89 - 86.53: 29 86.53 - 108.16: 4 Dihedral angle restraints: 10393 sinusoidal: 5495 harmonic: 4898 Sorted by residual: dihedral pdb=" C2' ADP A1602 " pdb=" C1' ADP A1602 " pdb=" N9 ADP A1602 " pdb=" C4 ADP A1602 " ideal model delta sinusoidal sigma weight residual 91.55 -160.30 -108.16 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" CA PRO A 267 " pdb=" C PRO A 267 " pdb=" N GLN A 268 " pdb=" CA GLN A 268 " ideal model delta harmonic sigma weight residual 180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 10390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1555 0.084 - 0.167: 88 0.167 - 0.251: 2 0.251 - 0.334: 0 0.334 - 0.418: 2 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA ARG A 517 " pdb=" N ARG A 517 " pdb=" C ARG A 517 " pdb=" CB ARG A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA ASP A 120 " pdb=" N ASP A 120 " pdb=" C ASP A 120 " pdb=" CB ASP A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA CYS A1411 " pdb=" N CYS A1411 " pdb=" C CYS A1411 " pdb=" CB CYS A1411 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1644 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 RHQ A1603 " 0.039 2.00e-02 2.50e+03 2.90e-01 2.31e+03 pdb=" C2 RHQ A1603 " -0.098 2.00e-02 2.50e+03 pdb=" C21 RHQ A1603 " 0.140 2.00e-02 2.50e+03 pdb=" C24 RHQ A1603 " -0.743 2.00e-02 2.50e+03 pdb=" C3 RHQ A1603 " -0.055 2.00e-02 2.50e+03 pdb=" C4 RHQ A1603 " 0.108 2.00e-02 2.50e+03 pdb=" C5 RHQ A1603 " 0.244 2.00e-02 2.50e+03 pdb=" C6 RHQ A1603 " 0.207 2.00e-02 2.50e+03 pdb=" C9 RHQ A1603 " -0.260 2.00e-02 2.50e+03 pdb=" N2 RHQ A1603 " 0.397 2.00e-02 2.50e+03 pdb=" O1 RHQ A1603 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 882 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" N GLU A 883 " 0.044 2.00e-02 2.50e+03 pdb=" CA GLU A 883 " -0.011 2.00e-02 2.50e+03 pdb=" H GLU A 883 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 808 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 809 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.029 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 946 2.18 - 2.78: 43433 2.78 - 3.39: 62624 3.39 - 3.99: 81584 3.99 - 4.60: 128101 Nonbonded interactions: 316688 Sorted by model distance: nonbonded pdb="HH12 ARG A 962 " pdb=" OE2 GLU A 987 " model vdw 1.572 2.450 nonbonded pdb=" O GLN A1182 " pdb="HE21 GLN A1187 " model vdw 1.573 2.450 nonbonded pdb=" OE1 GLU A 238 " pdb=" HZ2 LYS A 328 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLN A1044 " pdb=" H GLN A1044 " model vdw 1.612 2.450 nonbonded pdb=" HA ASP A 120 " pdb=" HB3 ASP A 120 " model vdw 1.634 1.952 ... (remaining 316683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 11.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.360 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 0.102 11188 Z= 0.308 Angle : 0.724 20.121 15176 Z= 0.455 Chirality : 0.042 0.418 1647 Planarity : 0.008 0.290 1905 Dihedral : 13.917 108.156 4041 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % 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: 0.57 (0.23), residues: 1341 helix: 1.03 (0.19), residues: 764 sheet: -0.17 (0.55), residues: 86 loop : -0.44 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 297 TYR 0.012 0.002 TYR A1335 PHE 0.021 0.002 PHE A 35 TRP 0.009 0.001 TRP A 451 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.31 (11185) covalent geometry : angle 0.72047 / 0.45 (15170) SS BOND : bond 0.00684 / 0.34 ( 3) SS BOND : angle 3.54668 / 3.44 ( 6) hydrogen bonds : bond 0.14966 / 10.08 ( 626) hydrogen bonds : angle 6.10460 / 4.30 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8069 (t80) cc_final: 0.7866 (t80) REVERT: A 580 GLU cc_start: 0.8178 (tt0) cc_final: 0.7906 (tt0) REVERT: A 1264 ASP cc_start: 0.7935 (m-30) cc_final: 0.7565 (m-30) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2549 time to fit residues: 40.1457 Evaluate side-chains 92 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN A1138 ASN A1198 GLN A1253 GLN A1456 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089975 restraints weight = 59315.886| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.12 r_work: 0.3156 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11188 Z= 0.164 Angle : 0.582 8.256 15176 Z= 0.304 Chirality : 0.041 0.397 1647 Planarity : 0.004 0.043 1905 Dihedral : 8.504 104.007 1536 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.60 % Allowed : 2.84 % Favored : 96.56 % 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: 0.77 (0.23), residues: 1341 helix: 1.24 (0.19), residues: 774 sheet: -0.29 (0.54), residues: 87 loop : -0.42 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 297 TYR 0.012 0.001 TYR A 291 PHE 0.014 0.001 PHE A 35 TRP 0.009 0.001 TRP A 451 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (11185) covalent geometry : angle 0.58190 / 0.30 (15170) SS BOND : bond 0.00377 / 0.19 ( 3) SS BOND : angle 1.11839 / 0.89 ( 6) hydrogen bonds : bond 0.05014 / 3.37 ( 626) hydrogen bonds : angle 5.01844 / 3.54 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 GLU cc_start: 0.8657 (tt0) cc_final: 0.8393 (tt0) REVERT: A 1264 ASP cc_start: 0.8501 (m-30) cc_final: 0.8051 (m-30) outliers start: 7 outliers final: 7 residues processed: 106 average time/residue: 0.2307 time to fit residues: 35.2686 Evaluate side-chains 101 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1044 GLN Chi-restraints excluded: chain A residue 1138 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.087112 restraints weight = 59585.920| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.03 r_work: 0.3107 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 11188 Z= 0.310 Angle : 0.626 8.494 15176 Z= 0.333 Chirality : 0.044 0.402 1647 Planarity : 0.004 0.043 1905 Dihedral : 8.724 99.619 1536 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.69 % Allowed : 5.42 % Favored : 93.89 % 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: 0.50 (0.23), residues: 1341 helix: 1.07 (0.19), residues: 776 sheet: -0.33 (0.55), residues: 87 loop : -0.66 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 297 TYR 0.019 0.002 TYR A 591 PHE 0.015 0.002 PHE A1210 TRP 0.010 0.001 TRP A 451 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.31 (11185) covalent geometry : angle 0.62549 / 0.33 (15170) SS BOND : bond 0.00758 / 0.38 ( 3) SS BOND : angle 1.60824 / 1.21 ( 6) hydrogen bonds : bond 0.05067 / 3.36 ( 626) hydrogen bonds : angle 4.98000 / 3.53 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8099 (t80) cc_final: 0.7818 (t80) REVERT: A 580 GLU cc_start: 0.8624 (tt0) cc_final: 0.8342 (tt0) REVERT: A 1264 ASP cc_start: 0.8464 (m-30) cc_final: 0.8011 (m-30) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.2211 time to fit residues: 31.8297 Evaluate side-chains 97 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN A1285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090301 restraints weight = 59266.547| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.12 r_work: 0.3175 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11188 Z= 0.133 Angle : 0.534 7.754 15176 Z= 0.276 Chirality : 0.040 0.397 1647 Planarity : 0.004 0.040 1905 Dihedral : 8.252 96.306 1536 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.69 % Allowed : 5.59 % Favored : 93.72 % 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: 0.83 (0.24), residues: 1341 helix: 1.33 (0.19), residues: 779 sheet: -0.39 (0.54), residues: 87 loop : -0.48 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.011 0.001 TYR A 591 PHE 0.011 0.001 PHE A 635 TRP 0.009 0.001 TRP A1200 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11185) covalent geometry : angle 0.53420 / 0.28 (15170) SS BOND : bond 0.00345 / 0.17 ( 3) SS BOND : angle 0.92563 / 0.72 ( 6) hydrogen bonds : bond 0.04177 / 2.78 ( 626) hydrogen bonds : angle 4.65975 / 3.30 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8126 (t80) cc_final: 0.7795 (t80) REVERT: A 580 GLU cc_start: 0.8647 (tt0) cc_final: 0.8374 (tt0) REVERT: A 1264 ASP cc_start: 0.8434 (m-30) cc_final: 0.7990 (m-30) outliers start: 8 outliers final: 7 residues processed: 103 average time/residue: 0.2193 time to fit residues: 32.6543 Evaluate side-chains 100 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN A1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.100851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088048 restraints weight = 59786.394| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.11 r_work: 0.3127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 11188 Z= 0.288 Angle : 0.597 7.914 15176 Z= 0.316 Chirality : 0.043 0.402 1647 Planarity : 0.004 0.041 1905 Dihedral : 8.485 94.517 1536 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.69 % Allowed : 6.97 % Favored : 92.34 % 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: 0.62 (0.23), residues: 1341 helix: 1.19 (0.19), residues: 779 sheet: -0.40 (0.55), residues: 87 loop : -0.65 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 276 TYR 0.018 0.002 TYR A 591 PHE 0.015 0.002 PHE A1242 TRP 0.009 0.001 TRP A1200 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.29 (11185) covalent geometry : angle 0.59635 / 0.32 (15170) SS BOND : bond 0.00708 / 0.36 ( 3) SS BOND : angle 1.41793 / 1.08 ( 6) hydrogen bonds : bond 0.04587 / 3.03 ( 626) hydrogen bonds : angle 4.77075 / 3.39 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8119 (t80) cc_final: 0.7804 (t80) REVERT: A 580 GLU cc_start: 0.8707 (tt0) cc_final: 0.8437 (tt0) REVERT: A 1264 ASP cc_start: 0.8468 (m-30) cc_final: 0.8029 (m-30) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.2356 time to fit residues: 33.7773 Evaluate side-chains 97 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1136 HIS Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090004 restraints weight = 58966.060| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.03 r_work: 0.3155 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11188 Z= 0.125 Angle : 0.520 7.662 15176 Z= 0.269 Chirality : 0.039 0.395 1647 Planarity : 0.004 0.039 1905 Dihedral : 8.112 91.741 1536 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.60 % Allowed : 7.31 % Favored : 92.08 % 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: 0.94 (0.24), residues: 1341 helix: 1.45 (0.19), residues: 779 sheet: -0.34 (0.55), residues: 87 loop : -0.49 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.012 0.001 TYR A 591 PHE 0.010 0.001 PHE A 255 TRP 0.008 0.001 TRP A1200 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (11185) covalent geometry : angle 0.52026 / 0.27 (15170) SS BOND : bond 0.00361 / 0.18 ( 3) SS BOND : angle 0.85711 / 0.65 ( 6) hydrogen bonds : bond 0.03949 / 2.62 ( 626) hydrogen bonds : angle 4.52571 / 3.21 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8107 (t80) cc_final: 0.7750 (t80) REVERT: A 528 LEU cc_start: 0.7423 (tp) cc_final: 0.7176 (mp) REVERT: A 580 GLU cc_start: 0.8674 (tt0) cc_final: 0.8408 (tt0) REVERT: A 1264 ASP cc_start: 0.8413 (m-30) cc_final: 0.7968 (m-30) outliers start: 7 outliers final: 7 residues processed: 102 average time/residue: 0.2140 time to fit residues: 32.5453 Evaluate side-chains 99 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 924 MET Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.102727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090711 restraints weight = 58652.100| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.03 r_work: 0.3170 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11188 Z= 0.112 Angle : 0.506 7.636 15176 Z= 0.259 Chirality : 0.039 0.394 1647 Planarity : 0.004 0.039 1905 Dihedral : 7.776 89.072 1536 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.34 % Allowed : 8.09 % Favored : 91.57 % 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: 1.17 (0.24), residues: 1341 helix: 1.67 (0.19), residues: 777 sheet: -0.36 (0.54), residues: 87 loop : -0.42 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 654 TYR 0.014 0.001 TYR A1414 PHE 0.010 0.001 PHE A 967 TRP 0.008 0.001 TRP A1200 HIS 0.002 0.000 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11185) covalent geometry : angle 0.50552 / 0.26 (15170) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 0.75783 / 0.59 ( 6) hydrogen bonds : bond 0.03724 / 2.46 ( 626) hydrogen bonds : angle 4.39909 / 3.12 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8093 (t80) cc_final: 0.7717 (t80) REVERT: A 528 LEU cc_start: 0.7452 (tp) cc_final: 0.7215 (mp) REVERT: A 580 GLU cc_start: 0.8664 (tt0) cc_final: 0.8398 (tt0) REVERT: A 1075 MET cc_start: 0.8431 (mmm) cc_final: 0.8201 (mmm) REVERT: A 1264 ASP cc_start: 0.8387 (m-30) cc_final: 0.7956 (m-30) outliers start: 4 outliers final: 4 residues processed: 101 average time/residue: 0.2479 time to fit residues: 36.7461 Evaluate side-chains 98 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 PHE Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 928 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.104946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092226 restraints weight = 58496.642| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11188 Z= 0.104 Angle : 0.493 7.595 15176 Z= 0.251 Chirality : 0.039 0.392 1647 Planarity : 0.003 0.039 1905 Dihedral : 7.497 88.675 1536 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.34 % Allowed : 8.43 % Favored : 91.22 % 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: 1.35 (0.24), residues: 1341 helix: 1.80 (0.19), residues: 780 sheet: -0.35 (0.54), residues: 87 loop : -0.33 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 654 TYR 0.010 0.001 TYR A1414 PHE 0.011 0.001 PHE A 967 TRP 0.007 0.001 TRP A1200 HIS 0.002 0.000 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (11185) covalent geometry : angle 0.49322 / 0.25 (15170) SS BOND : bond 0.00292 / 0.15 ( 3) SS BOND : angle 0.68298 / 0.55 ( 6) hydrogen bonds : bond 0.03543 / 2.34 ( 626) hydrogen bonds : angle 4.27904 / 3.03 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8133 (t80) cc_final: 0.7722 (t80) REVERT: A 528 LEU cc_start: 0.7501 (tp) cc_final: 0.7266 (mp) REVERT: A 580 GLU cc_start: 0.8684 (tt0) cc_final: 0.8422 (tt0) REVERT: A 1075 MET cc_start: 0.8412 (mmm) cc_final: 0.8164 (mmm) REVERT: A 1264 ASP cc_start: 0.8410 (m-30) cc_final: 0.7959 (m-30) outliers start: 4 outliers final: 3 residues processed: 108 average time/residue: 0.2702 time to fit residues: 41.6502 Evaluate side-chains 97 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 928 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.102463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089660 restraints weight = 59382.113| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.11 r_work: 0.3148 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11188 Z= 0.229 Angle : 0.554 7.801 15176 Z= 0.289 Chirality : 0.041 0.398 1647 Planarity : 0.004 0.058 1905 Dihedral : 7.799 87.847 1536 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.43 % Allowed : 9.04 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1341 helix: 1.62 (0.19), residues: 779 sheet: -0.27 (0.54), residues: 87 loop : -0.45 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 276 TYR 0.016 0.001 TYR A 591 PHE 0.014 0.002 PHE A1242 TRP 0.015 0.001 TRP A 451 HIS 0.003 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (11185) covalent geometry : angle 0.55363 / 0.29 (15170) SS BOND : bond 0.00594 / 0.30 ( 3) SS BOND : angle 1.14043 / 0.87 ( 6) hydrogen bonds : bond 0.04023 / 2.64 ( 626) hydrogen bonds : angle 4.45041 / 3.16 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8137 (t80) cc_final: 0.7756 (t80) REVERT: A 528 LEU cc_start: 0.7543 (tp) cc_final: 0.7284 (mp) REVERT: A 580 GLU cc_start: 0.8713 (tt0) cc_final: 0.8441 (tt0) REVERT: A 1075 MET cc_start: 0.8462 (mmm) cc_final: 0.8236 (mmm) REVERT: A 1264 ASP cc_start: 0.8427 (m-30) cc_final: 0.7997 (m-30) outliers start: 5 outliers final: 5 residues processed: 95 average time/residue: 0.2615 time to fit residues: 35.6769 Evaluate side-chains 95 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 952 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.104128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091394 restraints weight = 59019.087| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.12 r_work: 0.3178 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11188 Z= 0.122 Angle : 0.507 7.611 15176 Z= 0.260 Chirality : 0.039 0.396 1647 Planarity : 0.004 0.039 1905 Dihedral : 7.638 86.790 1536 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.26 % Allowed : 9.21 % Favored : 90.53 % 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: 1.25 (0.24), residues: 1341 helix: 1.73 (0.19), residues: 779 sheet: -0.34 (0.54), residues: 87 loop : -0.40 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 276 TYR 0.014 0.001 TYR A1414 PHE 0.010 0.001 PHE A 255 TRP 0.011 0.001 TRP A 451 HIS 0.002 0.000 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11185) covalent geometry : angle 0.50648 / 0.26 (15170) SS BOND : bond 0.00349 / 0.17 ( 3) SS BOND : angle 0.79795 / 0.61 ( 6) hydrogen bonds : bond 0.03672 / 2.42 ( 626) hydrogen bonds : angle 4.33593 / 3.08 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 882 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 TYR cc_start: 0.8139 (t80) cc_final: 0.7758 (t80) REVERT: A 528 LEU cc_start: 0.7551 (tp) cc_final: 0.7298 (mp) REVERT: A 580 GLU cc_start: 0.8704 (tt0) cc_final: 0.8443 (tt0) REVERT: A 1075 MET cc_start: 0.8439 (mmm) cc_final: 0.8207 (mmm) REVERT: A 1264 ASP cc_start: 0.8428 (m-30) cc_final: 0.7976 (m-30) outliers start: 3 outliers final: 3 residues processed: 100 average time/residue: 0.2607 time to fit residues: 37.4977 Evaluate side-chains 100 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 928 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091380 restraints weight = 58589.099| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.01 r_work: 0.3182 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11188 Z= 0.108 Angle : 0.497 7.660 15176 Z= 0.253 Chirality : 0.039 0.395 1647 Planarity : 0.004 0.044 1905 Dihedral : 7.354 88.520 1536 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.34 % Allowed : 9.04 % Favored : 90.62 % 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: 1.38 (0.24), residues: 1341 helix: 1.85 (0.19), residues: 780 sheet: -0.37 (0.53), residues: 87 loop : -0.36 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 276 TYR 0.014 0.001 TYR A1414 PHE 0.011 0.001 PHE A 967 TRP 0.012 0.001 TRP A 451 HIS 0.002 0.000 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11185) covalent geometry : angle 0.49668 / 0.25 (15170) SS BOND : bond 0.00308 / 0.15 ( 3) SS BOND : angle 0.70570 / 0.57 ( 6) hydrogen bonds : bond 0.03492 / 2.31 ( 626) hydrogen bonds : angle 4.24458 / 3.01 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4980.59 seconds wall clock time: 85 minutes 33.96 seconds (5133.96 seconds total)