Starting phenix.real_space_refine on Thu Sep 18 19:54:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.map" model { file = "/net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbf_11153/09_2025/6zbf_11153.cif" } resolution = 3.2 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= -0.002 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 6172 2.51 5 N 1571 2.21 5 O 1836 1.98 5 H 9861 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 9515 Classifications: {'peptide': 560} Link IDs: {'PTRANS': 14, 'TRANS': 545} Chain breaks: 4 Chain: "B" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1879 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "C" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4679 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Chain: "D" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 3386 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 2, 'TRANS': 197} Chain breaks: 1 Time building chain proxies: 3.62, per 1000 atoms: 0.19 Number of scatterers: 19459 At special positions: 0 Unit cell: (103.008, 136.271, 138.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 1836 8.00 N 1571 7.00 C 6172 6.00 H 9861 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.06 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=2.01 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: 1.75 Conformation dependent library (CDL) restraints added in 639.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.597A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.210A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.259A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.908A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.525A pdb=" N TYR A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.644A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.130A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.960A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.680A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.742A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.982A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.745A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.580A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.604A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.268A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.656A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'B' and resid 795 through 822 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.863A pdb=" N VAL B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.700A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.963A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.000A pdb=" N VAL C 966 " --> pdb=" O PRO C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.765A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1025 removed outlier: 3.602A pdb=" N LYS C1019 " --> pdb=" O ASN C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1033 through 1100 removed outlier: 3.530A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.724A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.040A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.638A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.522A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.530A pdb=" N LEU C1239 " --> pdb=" O GLU C1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1236 through 1239' Processing helix chain 'D' and resid 1342 through 1346 Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.618A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.648A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.606A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.681A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.551A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2112 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: 4.27 Time building geometry restraints manager: 2.51 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: 9859 1.04 - 1.23: 336 1.23 - 1.43: 3590 1.43 - 1.62: 5790 1.62 - 1.82: 32 Bond restraints: 19607 Sorted by residual: bond pdb=" C SER C1110 " pdb=" O SER C1110 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.18e-02 7.18e+03 1.71e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.484 -0.026 7.40e-03 1.83e+04 1.24e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE D1346 " pdb=" CA ILE D1346 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.21e-02 6.83e+03 1.12e+01 bond pdb=" N ILE D1552 " pdb=" CA ILE D1552 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 1.00e+01 ... (remaining 19602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 30408 1.61 - 3.22: 4884 3.22 - 4.84: 353 4.84 - 6.45: 64 6.45 - 8.06: 4 Bond angle restraints: 35713 Sorted by residual: angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.27 -5.91 1.09e+00 8.42e-01 2.94e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.98 7.02 1.30e+00 5.92e-01 2.91e+01 angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 115.06 5.86 1.12e+00 7.97e-01 2.73e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N LEU C1099 " pdb=" CA LEU C1099 " pdb=" C LEU C1099 " ideal model delta sigma weight residual 111.07 105.61 5.46 1.07e+00 8.73e-01 2.61e+01 ... (remaining 35708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8369 18.00 - 36.00: 542 36.00 - 53.99: 116 53.99 - 71.99: 27 71.99 - 89.99: 13 Dihedral angle restraints: 9067 sinusoidal: 5040 harmonic: 4027 Sorted by residual: dihedral pdb=" CB CYS B 813 " pdb=" SG CYS B 813 " pdb=" SG CYS B 845 " pdb=" CB CYS B 845 " ideal model delta sinusoidal sigma weight residual 93.00 147.92 -54.92 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CA ASP A 466 " pdb=" C ASP A 466 " pdb=" N ASN A 467 " pdb=" CA ASN A 467 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.99 -89.99 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 9064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 727 0.051 - 0.102: 478 0.102 - 0.153: 209 0.153 - 0.204: 49 0.204 - 0.255: 9 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA VAL C1105 " pdb=" N VAL C1105 " pdb=" C VAL C1105 " pdb=" CB VAL C1105 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL A 210 " pdb=" CA VAL A 210 " pdb=" CG1 VAL A 210 " pdb=" CG2 VAL A 210 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL D1345 " pdb=" CA VAL D1345 " pdb=" CG1 VAL D1345 " pdb=" CG2 VAL D1345 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1469 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 427 " 0.010 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" CG TYR A 427 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 427 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 427 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 427 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR A 427 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 427 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR A 427 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 427 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 427 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLN A 217 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1138 " -0.011 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" CG TYR C1138 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C1138 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C1138 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C1138 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C1138 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C1138 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C1138 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR C1138 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR C1138 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR C1138 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR C1138 " 0.005 2.00e-02 2.50e+03 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2122 2.28 - 2.86: 46124 2.86 - 3.44: 48333 3.44 - 4.02: 62538 4.02 - 4.60: 99417 Nonbonded interactions: 258534 Sorted by model distance: nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.698 2.450 nonbonded pdb=" OE2 GLU A 655 " pdb=" HG SER D1402 " model vdw 1.705 2.450 nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.716 2.450 nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.717 2.450 nonbonded pdb=" O THR C1050 " pdb=" HG SER C1054 " model vdw 1.720 2.450 ... (remaining 258529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.120 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.010 0.051 9748 Z= 0.735 Angle : 1.217 34.382 13078 Z= 0.864 Chirality : 0.075 0.255 1472 Planarity : 0.006 0.043 1643 Dihedral : 13.489 89.989 3828 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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 aren not related in a simple way. whole: 0.79 (0.24), residues: 1136 helix: 0.87 (0.16), residues: 894 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 225 TYR 0.041 0.003 TYR A 427 PHE 0.016 0.003 PHE C1055 HIS 0.007 0.002 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.01032 ( 9746) covalent geometry : angle 1.17373 (13074) SS BOND : bond 0.02170 ( 2) SS BOND : angle 18.44087 ( 4) hydrogen bonds : bond 0.16984 ( 718) hydrogen bonds : angle 5.81693 ( 2112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.8902 (mt) cc_final: 0.8608 (tt) REVERT: B 824 MET cc_start: 0.8622 (ttp) cc_final: 0.8346 (ttp) REVERT: B 866 ASP cc_start: 0.8118 (t0) cc_final: 0.7640 (t0) REVERT: C 1005 ASN cc_start: 0.8360 (m-40) cc_final: 0.7988 (m-40) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3168 time to fit residues: 89.4278 Evaluate side-chains 106 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.082521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067469 restraints weight = 102735.821| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.82 r_work: 0.3335 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9748 Z= 0.148 Angle : 0.575 6.055 13078 Z= 0.316 Chirality : 0.033 0.136 1472 Planarity : 0.003 0.044 1643 Dihedral : 4.200 21.652 1228 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.55 % Allowed : 7.82 % Favored : 91.64 % 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 aren not related in a simple way. whole: 1.60 (0.24), residues: 1136 helix: 1.46 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 146 TYR 0.014 0.001 TYR D1347 PHE 0.018 0.001 PHE A 163 HIS 0.008 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9746) covalent geometry : angle 0.57466 (13074) SS BOND : bond 0.00254 ( 2) SS BOND : angle 1.33184 ( 4) hydrogen bonds : bond 0.05845 ( 718) hydrogen bonds : angle 4.16773 ( 2112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9016 (mt) cc_final: 0.8716 (tt) REVERT: A 451 MET cc_start: 0.7755 (ttm) cc_final: 0.7146 (ttt) REVERT: A 497 LYS cc_start: 0.9046 (tttt) cc_final: 0.8740 (tptt) REVERT: B 846 ASP cc_start: 0.7133 (m-30) cc_final: 0.6573 (m-30) REVERT: B 852 PHE cc_start: 0.7653 (m-80) cc_final: 0.6920 (t80) REVERT: B 866 ASP cc_start: 0.8603 (t0) cc_final: 0.8143 (t0) REVERT: C 1005 ASN cc_start: 0.8315 (m-40) cc_final: 0.8047 (m-40) REVERT: C 1071 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7257 (ttpt) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 0.2290 time to fit residues: 35.0814 Evaluate side-chains 95 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain D residue 1465 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.064924 restraints weight = 105558.252| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.92 r_work: 0.3261 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9748 Z= 0.160 Angle : 0.519 5.537 13078 Z= 0.288 Chirality : 0.033 0.147 1472 Planarity : 0.003 0.035 1643 Dihedral : 3.952 16.561 1228 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % 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 aren not related in a simple way. whole: 2.24 (0.24), residues: 1136 helix: 1.92 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -0.25 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.013 0.001 TYR A 559 PHE 0.019 0.002 PHE A 534 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9746) covalent geometry : angle 0.51837 (13074) SS BOND : bond 0.01027 ( 2) SS BOND : angle 1.40845 ( 4) hydrogen bonds : bond 0.05146 ( 718) hydrogen bonds : angle 3.92968 ( 2112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9049 (mt) cc_final: 0.8763 (tt) REVERT: A 451 MET cc_start: 0.7861 (ttm) cc_final: 0.7152 (ttp) REVERT: B 846 ASP cc_start: 0.7493 (m-30) cc_final: 0.6919 (m-30) REVERT: B 852 PHE cc_start: 0.7849 (m-80) cc_final: 0.7028 (t80) REVERT: B 866 ASP cc_start: 0.8601 (t0) cc_final: 0.8212 (t0) REVERT: C 1014 PHE cc_start: 0.8461 (m-80) cc_final: 0.8247 (m-10) REVERT: C 1071 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7238 (ttpt) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.1992 time to fit residues: 30.2653 Evaluate side-chains 92 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain D residue 1375 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.065597 restraints weight = 105186.053| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.96 r_work: 0.3280 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9748 Z= 0.114 Angle : 0.470 6.070 13078 Z= 0.256 Chirality : 0.032 0.132 1472 Planarity : 0.003 0.034 1643 Dihedral : 3.750 17.497 1228 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.91 % Allowed : 8.64 % Favored : 90.45 % 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 aren not related in a simple way. whole: 2.84 (0.25), residues: 1136 helix: 2.35 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -0.01 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1384 TYR 0.012 0.001 TYR D1347 PHE 0.016 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9746) covalent geometry : angle 0.46694 (13074) SS BOND : bond 0.01452 ( 2) SS BOND : angle 3.21473 ( 4) hydrogen bonds : bond 0.04711 ( 718) hydrogen bonds : angle 3.69232 ( 2112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9072 (mt) cc_final: 0.8804 (tt) REVERT: A 497 LYS cc_start: 0.8989 (tttt) cc_final: 0.8609 (tptp) REVERT: A 534 PHE cc_start: 0.8370 (m-10) cc_final: 0.8137 (m-80) REVERT: B 846 ASP cc_start: 0.7472 (m-30) cc_final: 0.7020 (m-30) REVERT: B 852 PHE cc_start: 0.7803 (m-80) cc_final: 0.7023 (t80) REVERT: B 866 ASP cc_start: 0.8571 (t0) cc_final: 0.8084 (t0) REVERT: C 1016 ASP cc_start: 0.8567 (m-30) cc_final: 0.7363 (t70) REVERT: C 1071 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7185 (ttpt) REVERT: D 1339 PHE cc_start: 0.5661 (m-80) cc_final: 0.5270 (m-80) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.2401 time to fit residues: 33.6260 Evaluate side-chains 86 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.080637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065187 restraints weight = 104888.884| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.90 r_work: 0.3276 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9748 Z= 0.123 Angle : 0.464 9.148 13078 Z= 0.253 Chirality : 0.032 0.158 1472 Planarity : 0.002 0.033 1643 Dihedral : 3.752 35.230 1228 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.91 % Allowed : 8.73 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: 3.07 (0.25), residues: 1136 helix: 2.52 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.07 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.011 0.001 TYR D1347 PHE 0.012 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9746) covalent geometry : angle 0.46171 (13074) SS BOND : bond 0.00459 ( 2) SS BOND : angle 2.70785 ( 4) hydrogen bonds : bond 0.04511 ( 718) hydrogen bonds : angle 3.64565 ( 2112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9080 (mt) cc_final: 0.8834 (tt) REVERT: A 497 LYS cc_start: 0.8974 (tttt) cc_final: 0.8608 (tptp) REVERT: A 534 PHE cc_start: 0.8402 (m-10) cc_final: 0.8184 (m-80) REVERT: B 846 ASP cc_start: 0.7463 (m-30) cc_final: 0.7079 (m-30) REVERT: B 852 PHE cc_start: 0.7847 (m-80) cc_final: 0.7071 (t80) REVERT: B 866 ASP cc_start: 0.8582 (t0) cc_final: 0.8094 (t0) REVERT: C 1016 ASP cc_start: 0.8562 (m-30) cc_final: 0.7388 (t70) REVERT: D 1339 PHE cc_start: 0.5675 (m-80) cc_final: 0.5307 (m-80) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.2140 time to fit residues: 27.9784 Evaluate side-chains 87 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain D residue 1375 ASP Chi-restraints excluded: chain D residue 1554 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.080296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064825 restraints weight = 105199.052| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.91 r_work: 0.3266 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9748 Z= 0.122 Angle : 0.455 5.178 13078 Z= 0.248 Chirality : 0.032 0.130 1472 Planarity : 0.002 0.031 1643 Dihedral : 3.612 28.715 1228 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.82 % Allowed : 9.00 % Favored : 90.18 % 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 aren not related in a simple way. whole: 3.37 (0.25), residues: 1136 helix: 2.70 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.011 0.001 TYR D1347 PHE 0.012 0.001 PHE D1496 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9746) covalent geometry : angle 0.45454 (13074) SS BOND : bond 0.00544 ( 2) SS BOND : angle 1.40180 ( 4) hydrogen bonds : bond 0.04377 ( 718) hydrogen bonds : angle 3.58182 ( 2112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9112 (mt) cc_final: 0.8829 (tt) REVERT: A 451 MET cc_start: 0.7999 (ttm) cc_final: 0.7460 (ttt) REVERT: A 534 PHE cc_start: 0.8427 (m-10) cc_final: 0.8195 (m-80) REVERT: B 846 ASP cc_start: 0.7521 (m-30) cc_final: 0.7176 (m-30) REVERT: B 852 PHE cc_start: 0.7805 (m-80) cc_final: 0.7037 (t80) REVERT: B 866 ASP cc_start: 0.8589 (t0) cc_final: 0.8098 (t0) REVERT: C 1016 ASP cc_start: 0.8595 (m-30) cc_final: 0.7404 (t70) REVERT: D 1339 PHE cc_start: 0.5661 (m-80) cc_final: 0.5311 (m-80) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.2321 time to fit residues: 30.3503 Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain D residue 1375 ASP Chi-restraints excluded: chain D residue 1554 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.080256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.064772 restraints weight = 105397.292| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.89 r_work: 0.3265 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9748 Z= 0.116 Angle : 0.445 6.233 13078 Z= 0.243 Chirality : 0.031 0.130 1472 Planarity : 0.002 0.031 1643 Dihedral : 3.547 25.859 1228 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 9.45 % Favored : 90.00 % 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 aren not related in a simple way. whole: 3.51 (0.25), residues: 1136 helix: 2.79 (0.17), residues: 902 sheet: None (None), residues: 0 loop : 0.43 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.010 0.001 TYR D1347 PHE 0.011 0.001 PHE D1496 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9746) covalent geometry : angle 0.44428 (13074) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.04064 ( 4) hydrogen bonds : bond 0.04295 ( 718) hydrogen bonds : angle 3.55021 ( 2112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9112 (mt) cc_final: 0.8833 (tt) REVERT: A 451 MET cc_start: 0.8009 (ttm) cc_final: 0.7480 (ttt) REVERT: A 534 PHE cc_start: 0.8434 (m-10) cc_final: 0.8205 (m-80) REVERT: B 846 ASP cc_start: 0.7491 (m-30) cc_final: 0.7159 (m-30) REVERT: B 852 PHE cc_start: 0.7800 (m-80) cc_final: 0.7030 (t80) REVERT: B 866 ASP cc_start: 0.8586 (t0) cc_final: 0.8092 (t0) REVERT: B 881 GLN cc_start: 0.8779 (tt0) cc_final: 0.8509 (tt0) REVERT: C 1016 ASP cc_start: 0.8585 (m-30) cc_final: 0.7417 (t70) REVERT: D 1339 PHE cc_start: 0.5710 (m-80) cc_final: 0.5351 (m-80) outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.2088 time to fit residues: 27.3125 Evaluate side-chains 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain D residue 1375 ASP Chi-restraints excluded: chain D residue 1554 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.080656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065223 restraints weight = 104981.550| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.89 r_work: 0.3286 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9748 Z= 0.105 Angle : 0.437 5.486 13078 Z= 0.238 Chirality : 0.031 0.151 1472 Planarity : 0.002 0.032 1643 Dihedral : 3.493 23.430 1228 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.55 % Allowed : 9.82 % Favored : 89.64 % 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 aren not related in a simple way. whole: 3.70 (0.25), residues: 1136 helix: 2.92 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 0.46 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.010 0.001 TYR D1347 PHE 0.010 0.001 PHE D1496 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9746) covalent geometry : angle 0.43704 (13074) SS BOND : bond 0.00954 ( 2) SS BOND : angle 0.93995 ( 4) hydrogen bonds : bond 0.04151 ( 718) hydrogen bonds : angle 3.45623 ( 2112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 LEU cc_start: 0.9137 (mt) cc_final: 0.8851 (tt) REVERT: A 451 MET cc_start: 0.7952 (ttm) cc_final: 0.7434 (ttt) REVERT: A 497 LYS cc_start: 0.8935 (tttt) cc_final: 0.8479 (tptp) REVERT: B 846 ASP cc_start: 0.7511 (m-30) cc_final: 0.7187 (m-30) REVERT: B 852 PHE cc_start: 0.7789 (m-80) cc_final: 0.7020 (t80) REVERT: B 881 GLN cc_start: 0.8797 (tt0) cc_final: 0.8567 (tt0) REVERT: C 1016 ASP cc_start: 0.8576 (m-30) cc_final: 0.7434 (t70) REVERT: D 1339 PHE cc_start: 0.5725 (m-80) cc_final: 0.5363 (m-80) REVERT: D 1396 MET cc_start: 0.7898 (ptm) cc_final: 0.7686 (ptm) outliers start: 6 outliers final: 4 residues processed: 89 average time/residue: 0.1859 time to fit residues: 24.8054 Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain D residue 1375 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.079600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064107 restraints weight = 105675.672| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.87 r_work: 0.3249 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9748 Z= 0.143 Angle : 0.467 9.926 13078 Z= 0.255 Chirality : 0.032 0.129 1472 Planarity : 0.003 0.029 1643 Dihedral : 3.495 21.804 1228 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.55 % Allowed : 10.18 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.25), residues: 1136 helix: 2.87 (0.17), residues: 903 sheet: None (None), residues: 0 loop : 0.32 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.011 0.001 TYR B 865 PHE 0.014 0.001 PHE A 534 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9746) covalent geometry : angle 0.46696 (13074) SS BOND : bond 0.00586 ( 2) SS BOND : angle 1.35213 ( 4) hydrogen bonds : bond 0.04229 ( 718) hydrogen bonds : angle 3.58224 ( 2112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.9171 (t80) cc_final: 0.8864 (t80) REVERT: A 383 LEU cc_start: 0.9134 (mt) cc_final: 0.8853 (tt) REVERT: A 451 MET cc_start: 0.8037 (ttm) cc_final: 0.7245 (ttp) REVERT: A 497 LYS cc_start: 0.8940 (tttt) cc_final: 0.8467 (tptp) REVERT: A 534 PHE cc_start: 0.8503 (m-10) cc_final: 0.8287 (m-80) REVERT: B 846 ASP cc_start: 0.7502 (m-30) cc_final: 0.7233 (m-30) REVERT: B 852 PHE cc_start: 0.7869 (m-80) cc_final: 0.7116 (t80) REVERT: C 1016 ASP cc_start: 0.8588 (m-30) cc_final: 0.7455 (t70) REVERT: D 1339 PHE cc_start: 0.5744 (m-80) cc_final: 0.5370 (m-80) REVERT: D 1396 MET cc_start: 0.7921 (ptm) cc_final: 0.7698 (ptm) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1946 time to fit residues: 25.0689 Evaluate side-chains 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 981 ASN Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain D residue 1375 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.080526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.065018 restraints weight = 105811.962| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.90 r_work: 0.3269 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9748 Z= 0.104 Angle : 0.437 8.085 13078 Z= 0.236 Chirality : 0.031 0.130 1472 Planarity : 0.003 0.035 1643 Dihedral : 3.422 20.386 1228 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.27 % Allowed : 10.55 % Favored : 89.18 % 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 aren not related in a simple way. whole: 3.87 (0.25), residues: 1136 helix: 3.06 (0.17), residues: 901 sheet: None (None), residues: 0 loop : 0.47 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.009 0.001 TYR D1347 PHE 0.011 0.001 PHE A 534 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9746) covalent geometry : angle 0.43626 (13074) SS BOND : bond 0.00306 ( 2) SS BOND : angle 1.18644 ( 4) hydrogen bonds : bond 0.04043 ( 718) hydrogen bonds : angle 3.42546 ( 2112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.9096 (t80) cc_final: 0.8786 (t80) REVERT: A 383 LEU cc_start: 0.9165 (mt) cc_final: 0.8884 (tt) REVERT: A 451 MET cc_start: 0.7960 (ttm) cc_final: 0.7481 (ttt) REVERT: A 497 LYS cc_start: 0.8930 (tttt) cc_final: 0.8685 (tptt) REVERT: A 534 PHE cc_start: 0.8459 (m-10) cc_final: 0.8231 (m-80) REVERT: B 846 ASP cc_start: 0.7551 (m-30) cc_final: 0.7302 (m-30) REVERT: B 852 PHE cc_start: 0.7820 (m-80) cc_final: 0.7078 (t80) REVERT: C 1016 ASP cc_start: 0.8591 (m-30) cc_final: 0.7493 (t70) REVERT: C 1216 TYR cc_start: 0.8140 (t80) cc_final: 0.7920 (t80) REVERT: D 1339 PHE cc_start: 0.5783 (m-80) cc_final: 0.5385 (m-80) REVERT: D 1396 MET cc_start: 0.7877 (ptm) cc_final: 0.7655 (ptm) outliers start: 3 outliers final: 3 residues processed: 82 average time/residue: 0.1811 time to fit residues: 22.2654 Evaluate side-chains 82 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain C residue 1182 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.079969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064554 restraints weight = 106383.607| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.89 r_work: 0.3264 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9748 Z= 0.118 Angle : 0.447 8.615 13078 Z= 0.243 Chirality : 0.031 0.129 1472 Planarity : 0.003 0.033 1643 Dihedral : 3.421 19.306 1228 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.45 % Allowed : 10.36 % Favored : 89.18 % 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 aren not related in a simple way. whole: 3.84 (0.25), residues: 1136 helix: 3.04 (0.17), residues: 903 sheet: None (None), residues: 0 loop : 0.42 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.014 0.001 TYR A 186 PHE 0.011 0.001 PHE A 534 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9746) covalent geometry : angle 0.44620 (13074) SS BOND : bond 0.00363 ( 2) SS BOND : angle 1.24403 ( 4) hydrogen bonds : bond 0.04064 ( 718) hydrogen bonds : angle 3.47800 ( 2112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.47 seconds wall clock time: 72 minutes 28.52 seconds (4348.52 seconds total)