Starting phenix.real_space_refine on Thu Mar 5 11:29:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143.map" model { file = "/net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p04_13143/03_2026/7p04_13143_trim.cif" } resolution = 2.85 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 7022 2.51 5 N 1794 2.21 5 O 1979 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 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21543 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: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.44, per 1000 atoms: 0.16 Number of scatterers: 21543 At special positions: 0 Unit cell: (103.668, 95.844, 150.612, 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 1979 8.00 N 1794 7.00 C 7022 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=2.03 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: 1.79 Conformation dependent library (CDL) restraints added in 573.8 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: 62 helices and 7 sheets defined 62.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 36 through 56 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 103 through 117 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 232 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.825A 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 removed outlier: 3.808A pdb=" N ARG A 297 " --> pdb=" O SER A 294 " (cutoff:3.500A) 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 376 removed outlier: 4.106A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 4.639A pdb=" N LYS A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LYS A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) 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 removed outlier: 3.571A pdb=" N LYS A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.604A pdb=" N LYS A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 519 Processing helix chain 'A' and resid 519 through 541 removed outlier: 4.132A pdb=" N THR A 523 " --> pdb=" O ASN A 519 " (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 571 removed outlier: 4.692A pdb=" N SER A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 591 Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 595 through 607 removed outlier: 3.758A pdb=" N GLU A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 627 removed outlier: 3.886A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.611A pdb=" N THR A 660 " --> pdb=" O VAL A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 4.334A 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: 3.798A pdb=" N TRP A 698 " --> pdb=" O SER A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 716 removed outlier: 3.502A 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 816 removed outlier: 4.026A pdb=" N ARG A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 919 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 960 through 973 Processing helix chain 'A' and resid 978 through 993 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1042 through 1060 Processing helix chain 'A' and resid 1071 through 1077 removed outlier: 3.845A pdb=" N GLU A1077 " --> pdb=" O ILE A1073 " (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 1109 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.733A pdb=" N VAL A1144 " --> pdb=" O ASP A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1164 removed outlier: 3.740A 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: 3.865A pdb=" N THR A1245 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1269 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1306 removed outlier: 3.644A pdb=" N GLU A1289 " --> pdb=" O GLN A1285 " (cutoff:3.500A) Proline residue: A1291 - end of helix removed outlier: 4.264A pdb=" N TYR A1306 " --> pdb=" O PHE A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1317 removed outlier: 3.503A pdb=" N ASN A1313 " --> pdb=" O GLY A1309 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A1317 " --> pdb=" O ASN A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1349 removed outlier: 4.408A pdb=" N PHE A1348 " --> pdb=" O LEU A1344 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A1349 " --> pdb=" O VAL A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1369 removed outlier: 3.558A pdb=" N ALA A1355 " --> pdb=" O VAL A1351 " (cutoff:3.500A) 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: 4.229A pdb=" N TYR A1394 " --> pdb=" O SER A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 Proline residue: A1433 - end of helix Processing helix chain 'A' and resid 1459 through 1468 removed outlier: 3.543A pdb=" N ASN A1466 " --> pdb=" O ASP A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1472 No H-bonds generated for 'chain 'A' and resid 1470 through 1472' Processing helix chain 'A' and resid 1473 through 1500 Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 183 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 176 removed outlier: 6.411A pdb=" N ALA A 136 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.336A pdb=" N GLN A 330 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA A 365 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP A 332 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 390 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP A 384 " --> pdb=" O GLN A 388 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLN A 388 " --> pdb=" O ASP A 384 " (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: 7.479A pdb=" N ILE A 887 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N VAL A 878 " --> pdb=" O ILE A 887 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASN A 889 " --> pdb=" O TYR A 876 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TYR A 876 " --> pdb=" O ASN A 889 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 893 " --> pdb=" O ARG A 872 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG A 872 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 895 " --> pdb=" O HIS A 870 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS A 870 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 874 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR A 928 " --> pdb=" O LEU A 874 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR A 876 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 926 " --> pdb=" O TYR A 876 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 946 through 949 removed outlier: 6.479A pdb=" N VAL A1032 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A1066 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A1034 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN A1085 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR A1090 " --> pdb=" O GLN A1085 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1417 through 1419 removed outlier: 3.632A pdb=" N PHE A1419 " --> pdb=" O CYS A1452 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1794 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: 5.22 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10653 1.03 - 1.23: 48 1.23 - 1.42: 4809 1.42 - 1.62: 6206 1.62 - 1.81: 108 Bond restraints: 21824 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 6.35e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.88e+01 bond pdb=" C5 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.32e+01 bond pdb=" C4 ATP A1601 " pdb=" N9 ATP A1601 " ideal model delta sigma weight residual 1.374 1.329 0.045 1.00e-02 1.00e+04 2.00e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.354 -0.044 1.00e-02 1.00e+04 1.93e+01 ... (remaining 21819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.98: 39262 6.98 - 13.97: 7 13.97 - 20.95: 2 20.95 - 27.94: 0 27.94 - 34.92: 6 Bond angle restraints: 39277 Sorted by residual: angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 122.01 17.86 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 122.54 14.29 1.00e+00 1.00e+00 2.04e+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 75.08 34.92 3.00e+00 1.11e-01 1.36e+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 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ARG A 517 " pdb=" CA ARG A 517 " pdb=" HA ARG A 517 " ideal model delta sigma weight residual 110.00 75.45 34.55 3.00e+00 1.11e-01 1.33e+02 ... (remaining 39272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.84: 9735 21.84 - 43.68: 492 43.68 - 65.52: 131 65.52 - 87.35: 21 87.35 - 109.19: 5 Dihedral angle restraints: 10384 sinusoidal: 5486 harmonic: 4898 Sorted by residual: dihedral pdb=" CA TYR A1199 " pdb=" C TYR A1199 " pdb=" N TRP A1200 " pdb=" CA TRP A1200 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 49.19 -109.19 1 2.00e+01 2.50e-03 3.19e+01 dihedral pdb=" C4' ADP A1602 " pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual 180.00 75.72 104.28 1 2.00e+01 2.50e-03 2.99e+01 ... (remaining 10381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1589 0.093 - 0.186: 56 0.186 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 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 2.04 0.47 2.00e-01 2.50e+01 5.43e+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 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CA TYR A 591 " pdb=" N TYR A 591 " pdb=" C TYR A 591 " pdb=" CB TYR A 591 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1644 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 808 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.44e+00 pdb=" N PRO A 809 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 809 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 809 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1256 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A1257 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 685 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 686 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " 0.020 5.00e-02 4.00e+02 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1498 2.20 - 2.80: 45351 2.80 - 3.40: 62202 3.40 - 4.00: 82505 4.00 - 4.60: 127467 Nonbonded interactions: 319023 Sorted by model distance: nonbonded pdb="HH22 ARG A 872 " pdb=" OD1 ASP A1159 " model vdw 1.602 2.450 nonbonded pdb=" O ARG A1388 " pdb=" HH TYR A1394 " model vdw 1.609 2.450 nonbonded pdb=" HH TYR A 732 " pdb=" O TYR A1430 " model vdw 1.612 2.450 nonbonded pdb=" H ASP A 120 " pdb=" HA ASP A 120 " model vdw 1.612 1.816 nonbonded pdb=" HG SER A 597 " pdb=" OE1 GLU A 794 " model vdw 1.613 2.450 ... (remaining 319018 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: 12.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.700 Find NCS groups from input model: 0.100 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:7.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.005 0.080 11152 Z= 0.252 Angle : 0.660 17.859 15125 Z= 0.404 Chirality : 0.043 0.466 1647 Planarity : 0.004 0.063 1901 Dihedral : 14.228 109.192 4032 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -0.21 (0.23), residues: 1341 helix: 0.42 (0.18), residues: 771 sheet: -1.29 (0.47), residues: 105 loop : -0.62 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 48 TYR 0.016 0.002 TYR A1394 PHE 0.015 0.002 PHE A1242 TRP 0.009 0.001 TRP A 131 HIS 0.004 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00497 (11149) covalent geometry : angle 0.65895 (15119) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.78213 ( 6) hydrogen bonds : bond 0.12686 ( 618) hydrogen bonds : angle 5.66238 ( 1794) *********************** 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 154 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8266 (tppp) cc_final: 0.8048 (ttmt) REVERT: A 1031 LEU cc_start: 0.8282 (mp) cc_final: 0.8080 (mt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 1.1959 time to fit residues: 198.8637 Evaluate side-chains 107 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 281 ASN A 330 GLN A1456 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100860 restraints weight = 48543.866| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.00 r_work: 0.3211 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 11152 Z= 0.208 Angle : 0.604 7.763 15125 Z= 0.320 Chirality : 0.043 0.467 1647 Planarity : 0.004 0.057 1901 Dihedral : 8.737 102.343 1527 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.86 % Allowed : 7.83 % Favored : 91.31 % Cbeta Deviations : 0.08 % 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: -0.01 (0.23), residues: 1341 helix: 0.64 (0.18), residues: 779 sheet: -1.32 (0.47), residues: 105 loop : -0.63 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.014 0.002 TYR A1394 PHE 0.016 0.002 PHE A1242 TRP 0.007 0.001 TRP A 131 HIS 0.005 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00469 (11149) covalent geometry : angle 0.60301 (15119) SS BOND : bond 0.00467 ( 3) SS BOND : angle 1.42666 ( 6) hydrogen bonds : bond 0.05203 ( 618) hydrogen bonds : angle 4.88125 ( 1794) *********************** 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 123 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7736 (ttp-170) cc_final: 0.7390 (mtp180) REVERT: A 114 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7040 (tt) REVERT: A 462 LYS cc_start: 0.8477 (tppp) cc_final: 0.8011 (ttmt) REVERT: A 513 MET cc_start: 0.8339 (mmm) cc_final: 0.8109 (mmm) REVERT: A 517 ARG cc_start: 0.6558 (ptp-170) cc_final: 0.5298 (ppt-90) outliers start: 10 outliers final: 4 residues processed: 121 average time/residue: 1.1784 time to fit residues: 154.4833 Evaluate side-chains 108 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1370 CYS Chi-restraints excluded: chain A residue 1436 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102667 restraints weight = 47995.131| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.03 r_work: 0.3242 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11152 Z= 0.124 Angle : 0.534 7.646 15125 Z= 0.279 Chirality : 0.040 0.439 1647 Planarity : 0.004 0.061 1901 Dihedral : 7.949 110.927 1527 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.77 % Allowed : 9.64 % Favored : 89.59 % Cbeta Deviations : 0.08 % 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: 0.46 (0.23), residues: 1341 helix: 1.00 (0.19), residues: 785 sheet: -1.08 (0.48), residues: 105 loop : -0.42 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1146 TYR 0.011 0.001 TYR A 732 PHE 0.011 0.001 PHE A1242 TRP 0.007 0.001 TRP A 107 HIS 0.004 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00257 (11149) covalent geometry : angle 0.53341 (15119) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.77519 ( 6) hydrogen bonds : bond 0.04314 ( 618) hydrogen bonds : angle 4.53050 ( 1794) *********************** 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 126 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7725 (ttp-170) cc_final: 0.7394 (mtp180) REVERT: A 114 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6988 (tt) REVERT: A 419 THR cc_start: 0.8229 (m) cc_final: 0.7923 (p) REVERT: A 513 MET cc_start: 0.8303 (mmm) cc_final: 0.8037 (mmm) REVERT: A 517 ARG cc_start: 0.6609 (ptp-170) cc_final: 0.5368 (ppt-90) REVERT: A 765 GLN cc_start: 0.8207 (mt0) cc_final: 0.7961 (mm-40) outliers start: 9 outliers final: 3 residues processed: 124 average time/residue: 1.2249 time to fit residues: 164.3242 Evaluate side-chains 110 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1370 CYS Chi-restraints excluded: chain A residue 1432 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 127 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN A 642 ASN A1436 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.102245 restraints weight = 47959.484| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.03 r_work: 0.3247 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11152 Z= 0.143 Angle : 0.543 9.048 15125 Z= 0.282 Chirality : 0.040 0.437 1647 Planarity : 0.004 0.058 1901 Dihedral : 7.702 112.124 1527 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.20 % Allowed : 10.41 % Favored : 88.38 % Cbeta Deviations : 0.08 % 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: 0.66 (0.23), residues: 1341 helix: 1.19 (0.19), residues: 790 sheet: -1.05 (0.48), residues: 105 loop : -0.41 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.017 0.001 TYR A1151 PHE 0.011 0.001 PHE A 785 TRP 0.006 0.001 TRP A 451 HIS 0.004 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00317 (11149) covalent geometry : angle 0.54326 (15119) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.91191 ( 6) hydrogen bonds : bond 0.04173 ( 618) hydrogen bonds : angle 4.40928 ( 1794) *********************** 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 127 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.513 Fit side-chains REVERT: A 42 ARG cc_start: 0.7742 (ttp-170) cc_final: 0.7405 (mtp85) REVERT: A 114 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7082 (tt) REVERT: A 419 THR cc_start: 0.8213 (m) cc_final: 0.7903 (p) REVERT: A 513 MET cc_start: 0.8317 (mmm) cc_final: 0.8039 (mmm) REVERT: A 517 ARG cc_start: 0.6616 (ptp-170) cc_final: 0.5346 (ppt-90) REVERT: A 765 GLN cc_start: 0.8221 (mt0) cc_final: 0.7980 (mm-40) outliers start: 14 outliers final: 5 residues processed: 122 average time/residue: 1.2191 time to fit residues: 160.8491 Evaluate side-chains 109 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1341 MET Chi-restraints excluded: chain A residue 1370 CYS Chi-restraints excluded: chain A residue 1432 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN A1436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103131 restraints weight = 47742.675| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.02 r_work: 0.3255 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11152 Z= 0.118 Angle : 0.519 7.663 15125 Z= 0.269 Chirality : 0.040 0.432 1647 Planarity : 0.004 0.047 1901 Dihedral : 7.425 110.039 1527 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.29 % Allowed : 10.84 % Favored : 87.87 % Cbeta Deviations : 0.08 % 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: 0.87 (0.24), residues: 1341 helix: 1.34 (0.19), residues: 788 sheet: -1.01 (0.48), residues: 105 loop : -0.27 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.012 0.001 TYR A1142 PHE 0.011 0.001 PHE A 653 TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00256 (11149) covalent geometry : angle 0.51875 (15119) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.69063 ( 6) hydrogen bonds : bond 0.03935 ( 618) hydrogen bonds : angle 4.30783 ( 1794) *********************** 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 131 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.460 Fit side-chains REVERT: A 114 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7062 (tt) REVERT: A 419 THR cc_start: 0.8170 (m) cc_final: 0.7845 (p) REVERT: A 513 MET cc_start: 0.8302 (mmm) cc_final: 0.8040 (mmm) REVERT: A 517 ARG cc_start: 0.6631 (ptp-170) cc_final: 0.5418 (tmm160) REVERT: A 765 GLN cc_start: 0.8218 (mt0) cc_final: 0.7983 (mm-40) outliers start: 15 outliers final: 5 residues processed: 125 average time/residue: 1.1292 time to fit residues: 153.2742 Evaluate side-chains 111 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1370 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 132 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1237 GLN A1436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100651 restraints weight = 48332.404| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.02 r_work: 0.3218 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11152 Z= 0.225 Angle : 0.573 8.070 15125 Z= 0.301 Chirality : 0.042 0.443 1647 Planarity : 0.004 0.049 1901 Dihedral : 7.758 114.093 1527 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.12 % Allowed : 11.79 % Favored : 87.09 % Cbeta Deviations : 0.08 % 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: 0.58 (0.23), residues: 1341 helix: 1.10 (0.18), residues: 791 sheet: -1.08 (0.49), residues: 105 loop : -0.40 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.017 0.002 TYR A1394 PHE 0.017 0.002 PHE A1242 TRP 0.007 0.001 TRP A 131 HIS 0.004 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00518 (11149) covalent geometry : angle 0.57288 (15119) SS BOND : bond 0.00524 ( 3) SS BOND : angle 1.20712 ( 6) hydrogen bonds : bond 0.04407 ( 618) hydrogen bonds : angle 4.38918 ( 1794) *********************** 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 123 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7111 (tt) REVERT: A 419 THR cc_start: 0.8243 (m) cc_final: 0.7946 (p) REVERT: A 445 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8518 (tmmt) REVERT: A 462 LYS cc_start: 0.8456 (tppp) cc_final: 0.8007 (ttmt) REVERT: A 517 ARG cc_start: 0.6575 (ptp-170) cc_final: 0.5444 (tmm160) REVERT: A 765 GLN cc_start: 0.8241 (mt0) cc_final: 0.7981 (mm-40) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 1.1195 time to fit residues: 143.7674 Evaluate side-chains 114 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1370 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101845 restraints weight = 48097.590| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.02 r_work: 0.3232 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11152 Z= 0.145 Angle : 0.530 7.674 15125 Z= 0.276 Chirality : 0.040 0.435 1647 Planarity : 0.004 0.049 1901 Dihedral : 7.474 110.915 1527 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.20 % Allowed : 12.05 % Favored : 86.75 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1341 helix: 1.24 (0.19), residues: 791 sheet: -1.01 (0.49), residues: 105 loop : -0.33 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.013 0.001 TYR A1394 PHE 0.011 0.001 PHE A1369 TRP 0.006 0.001 TRP A 451 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00328 (11149) covalent geometry : angle 0.52976 (15119) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.85017 ( 6) hydrogen bonds : bond 0.04053 ( 618) hydrogen bonds : angle 4.29777 ( 1794) *********************** 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 124 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8433 (tppp) cc_final: 0.7981 (ttmt) REVERT: A 513 MET cc_start: 0.8341 (mmm) cc_final: 0.8128 (mmm) REVERT: A 517 ARG cc_start: 0.6633 (ptp-170) cc_final: 0.5415 (tmm160) REVERT: A 765 GLN cc_start: 0.8209 (mt0) cc_final: 0.7982 (mm-40) outliers start: 14 outliers final: 7 residues processed: 117 average time/residue: 1.0977 time to fit residues: 140.0511 Evaluate side-chains 114 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1341 MET Chi-restraints excluded: chain A residue 1370 CYS Chi-restraints excluded: chain A residue 1399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.117623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101562 restraints weight = 48316.272| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.02 r_work: 0.3232 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11152 Z= 0.163 Angle : 0.540 7.762 15125 Z= 0.282 Chirality : 0.041 0.435 1647 Planarity : 0.004 0.048 1901 Dihedral : 7.369 109.102 1527 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.12 % Allowed : 12.48 % Favored : 86.40 % Cbeta Deviations : 0.08 % 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: 0.80 (0.23), residues: 1341 helix: 1.28 (0.19), residues: 791 sheet: -0.94 (0.49), residues: 105 loop : -0.33 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.013 0.001 TYR A1394 PHE 0.016 0.001 PHE A1242 TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00370 (11149) covalent geometry : angle 0.54005 (15119) SS BOND : bond 0.00392 ( 3) SS BOND : angle 0.98618 ( 6) hydrogen bonds : bond 0.04078 ( 618) hydrogen bonds : angle 4.28023 ( 1794) *********************** 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 120 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.6924 (tt0) cc_final: 0.6678 (tt0) REVERT: A 462 LYS cc_start: 0.8439 (tppp) cc_final: 0.7984 (ttmt) REVERT: A 513 MET cc_start: 0.8336 (mmm) cc_final: 0.8114 (mmm) REVERT: A 517 ARG cc_start: 0.6594 (ptp-170) cc_final: 0.5425 (tmm160) REVERT: A 765 GLN cc_start: 0.8218 (mt0) cc_final: 0.7986 (mm-40) REVERT: A 1005 VAL cc_start: 0.8437 (t) cc_final: 0.8111 (m) outliers start: 13 outliers final: 6 residues processed: 113 average time/residue: 1.1173 time to fit residues: 137.7062 Evaluate side-chains 111 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1370 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 63 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1178 HIS A1436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100613 restraints weight = 48475.335| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.02 r_work: 0.3219 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11152 Z= 0.214 Angle : 0.568 7.865 15125 Z= 0.299 Chirality : 0.042 0.441 1647 Planarity : 0.004 0.046 1901 Dihedral : 7.561 108.974 1527 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.77 % Allowed : 12.99 % Favored : 86.23 % Cbeta Deviations : 0.08 % 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: 0.63 (0.23), residues: 1341 helix: 1.15 (0.18), residues: 791 sheet: -1.00 (0.49), residues: 105 loop : -0.42 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 337 TYR 0.016 0.002 TYR A1394 PHE 0.019 0.002 PHE A1242 TRP 0.006 0.001 TRP A 451 HIS 0.004 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00493 (11149) covalent geometry : angle 0.56763 (15119) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.19298 ( 6) hydrogen bonds : bond 0.04322 ( 618) hydrogen bonds : angle 4.34810 ( 1794) *********************** 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 115 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 56 GLN cc_start: 0.6849 (tt0) cc_final: 0.6588 (tt0) REVERT: A 462 LYS cc_start: 0.8442 (tppp) cc_final: 0.7994 (ttmt) REVERT: A 513 MET cc_start: 0.8342 (mmm) cc_final: 0.8102 (mmm) REVERT: A 517 ARG cc_start: 0.6584 (ptp-170) cc_final: 0.5369 (tmm160) REVERT: A 765 GLN cc_start: 0.8229 (mt0) cc_final: 0.7995 (mm-40) REVERT: A 1399 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8687 (mp) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 1.1159 time to fit residues: 133.5356 Evaluate side-chains 113 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1370 CYS Chi-restraints excluded: chain A residue 1399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103067 restraints weight = 47807.739| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.02 r_work: 0.3254 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11152 Z= 0.110 Angle : 0.518 7.372 15125 Z= 0.269 Chirality : 0.040 0.430 1647 Planarity : 0.004 0.047 1901 Dihedral : 7.091 105.140 1527 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.86 % Allowed : 12.99 % Favored : 86.14 % Cbeta Deviations : 0.08 % 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: 1.43 (0.19), residues: 791 sheet: -0.95 (0.49), residues: 106 loop : -0.32 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 337 TYR 0.011 0.001 TYR A 732 PHE 0.015 0.001 PHE A 542 TRP 0.007 0.001 TRP A1200 HIS 0.003 0.001 HIS A 295 Details of bonding type rmsd covalent geometry : bond 0.00238 (11149) covalent geometry : angle 0.51746 (15119) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.67904 ( 6) hydrogen bonds : bond 0.03813 ( 618) hydrogen bonds : angle 4.21626 ( 1794) ********************** 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 116 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.6879 (tt0) cc_final: 0.6584 (tt0) REVERT: A 462 LYS cc_start: 0.8421 (tppp) cc_final: 0.7964 (ttmt) REVERT: A 513 MET cc_start: 0.8327 (mmm) cc_final: 0.8123 (mmm) REVERT: A 517 ARG cc_start: 0.6604 (ptp-170) cc_final: 0.5319 (tmm160) REVERT: A 765 GLN cc_start: 0.8206 (mt0) cc_final: 0.7975 (mm-40) outliers start: 10 outliers final: 5 residues processed: 111 average time/residue: 1.1013 time to fit residues: 133.2241 Evaluate side-chains 106 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 1031 LEU Chi-restraints excluded: chain A residue 1370 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 0.0870 chunk 86 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103629 restraints weight = 47836.151| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.03 r_work: 0.3253 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11152 Z= 0.113 Angle : 0.512 7.671 15125 Z= 0.264 Chirality : 0.039 0.426 1647 Planarity : 0.004 0.045 1901 Dihedral : 6.778 102.558 1527 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.52 % Allowed : 13.34 % Favored : 86.14 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1341 helix: 1.65 (0.19), residues: 789 sheet: -0.80 (0.49), residues: 105 loop : -0.22 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.009 0.001 TYR A 732 PHE 0.011 0.001 PHE A1242 TRP 0.006 0.001 TRP A 451 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00252 (11149) covalent geometry : angle 0.51217 (15119) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.76966 ( 6) hydrogen bonds : bond 0.03675 ( 618) hydrogen bonds : angle 4.13089 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6464.20 seconds wall clock time: 110 minutes 7.00 seconds (6607.00 seconds total)