Starting phenix.real_space_refine on Thu Sep 18 20:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbe_11152/09_2025/6zbe_11152.map" } resolution = 3.3 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 6194 2.51 5 N 1577 2.21 5 O 1842 1.98 5 H 9902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 19534 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9553 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 14, 'TRANS': 547} Chain breaks: 4 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1901 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} 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: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3401 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 3.38, per 1000 atoms: 0.17 Number of scatterers: 19534 At special positions: 0 Unit cell: (101.935, 135.198, 139.49, 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 1842 8.00 N 1577 7.00 C 6194 6.00 H 9902 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=2.07 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " 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: 1.73 Conformation dependent library (CDL) restraints added in 606.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.593A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.203A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.271A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.915A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.504A 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: 3.638A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.351A 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: 4.126A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.951A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.686A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.903A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 464 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.985A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.743A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.589A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.597A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.270A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.634A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.873A 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: 3.703A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.959A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.002A 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: 3.774A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.252A 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 1101 removed outlier: 3.547A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.710A 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: 4.086A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.064A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.642A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1210 " --> pdb=" O GLU C1206 " (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: 3.536A 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: 3.503A pdb=" N LEU D1351 " --> pdb=" O TYR D1347 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.650A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.610A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.688A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.552A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2109 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: 3.78 Time building geometry restraints manager: 2.46 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: 9900 1.04 - 1.23: 282 1.23 - 1.43: 3647 1.43 - 1.62: 5821 1.62 - 1.82: 32 Bond restraints: 19682 Sorted by residual: bond pdb=" CG ASP A 37 " pdb=" OD1 ASP A 37 " ideal model delta sigma weight residual 1.249 1.179 0.070 1.90e-02 2.77e+03 1.37e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.484 -0.027 7.40e-03 1.83e+04 1.30e+01 bond pdb=" N VAL B 819 " pdb=" CA VAL B 819 " ideal model delta sigma weight residual 1.460 1.503 -0.043 1.19e-02 7.06e+03 1.29e+01 bond pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 1.454 1.482 -0.028 7.70e-03 1.69e+04 1.28e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 19677 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 30667 1.63 - 3.25: 4768 3.25 - 4.88: 348 4.88 - 6.51: 67 6.51 - 8.14: 4 Bond angle restraints: 35854 Sorted by residual: angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 114.73 6.19 1.12e+00 7.97e-01 3.06e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.26 6.02 1.09e+00 8.42e-01 3.05e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.99 7.01 1.30e+00 5.92e-01 2.91e+01 angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.20 -5.84 1.09e+00 8.42e-01 2.87e+01 angle pdb=" N PHE C1014 " pdb=" CA PHE C1014 " pdb=" C PHE C1014 " ideal model delta sigma weight residual 111.28 105.72 5.56 1.09e+00 8.42e-01 2.60e+01 ... (remaining 35849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8416 17.98 - 35.96: 523 35.96 - 53.93: 116 53.93 - 71.91: 30 71.91 - 89.89: 14 Dihedral angle restraints: 9099 sinusoidal: 5060 harmonic: 4039 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 93.00 148.29 -55.29 1 1.00e+01 1.00e-02 4.13e+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 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+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 89.89 -89.89 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 9096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 798 0.056 - 0.113: 490 0.113 - 0.169: 154 0.169 - 0.225: 30 0.225 - 0.281: 5 Chirality restraints: 1477 Sorted by residual: chirality pdb=" CB VAL B 819 " pdb=" CA VAL B 819 " pdb=" CG1 VAL B 819 " pdb=" CG2 VAL B 819 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.98e+00 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 1.66e+00 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1474 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.015 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C GLN A 217 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 327 " -0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C ASN A 327 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 327 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 328 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 328 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C GLU A 328 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU A 328 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 329 " -0.015 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 2078 2.28 - 2.86: 46251 2.86 - 3.44: 48340 3.44 - 4.02: 62481 4.02 - 4.60: 99520 Nonbonded interactions: 258670 Sorted by model distance: nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.697 2.450 nonbonded pdb=" O THR C1050 " pdb=" HG SER C1054 " model vdw 1.715 2.450 nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.716 2.450 nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.718 2.450 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.721 2.450 ... (remaining 258665 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: 1.560 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 0.070 9782 Z= 0.719 Angle : 1.209 35.145 13122 Z= 0.853 Chirality : 0.075 0.281 1477 Planarity : 0.006 0.043 1648 Dihedral : 13.395 89.889 3844 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.13 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: 0.61 (0.23), residues: 1140 helix: 0.75 (0.16), residues: 906 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 546 TYR 0.026 0.003 TYR A 683 PHE 0.017 0.003 PHE A 585 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.01012 ( 9780) covalent geometry : angle 1.16441 (13118) SS BOND : bond 0.02972 ( 2) SS BOND : angle 18.72036 ( 4) hydrogen bonds : bond 0.16685 ( 716) hydrogen bonds : angle 5.75089 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.579 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: 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 37 ASP cc_start: 0.9110 (t0) cc_final: 0.8469 (m-30) REVERT: A 303 TYR cc_start: 0.8579 (m-80) cc_final: 0.8362 (m-10) REVERT: A 441 ASP cc_start: 0.8545 (t70) cc_final: 0.8327 (m-30) REVERT: A 697 PHE cc_start: 0.7284 (t80) cc_final: 0.6970 (t80) REVERT: B 812 ILE cc_start: 0.8336 (mt) cc_final: 0.8072 (tt) REVERT: C 1014 PHE cc_start: 0.8744 (t80) cc_final: 0.8389 (t80) REVERT: D 1466 ILE cc_start: 0.9169 (pt) cc_final: 0.8940 (mt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2685 time to fit residues: 84.7826 Evaluate side-chains 105 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN C1077 GLN C1081 GLN D1341 ASN D1419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.081033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064813 restraints weight = 105456.225| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.84 r_work: 0.3267 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9782 Z= 0.153 Angle : 0.554 6.912 13122 Z= 0.308 Chirality : 0.034 0.131 1477 Planarity : 0.004 0.042 1648 Dihedral : 4.227 20.906 1232 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.18 % Allowed : 6.88 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.24), residues: 1140 helix: 1.48 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -0.47 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.012 0.001 TYR A 559 PHE 0.017 0.002 PHE A 163 HIS 0.007 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9780) covalent geometry : angle 0.55208 (13118) SS BOND : bond 0.01812 ( 2) SS BOND : angle 2.47384 ( 4) hydrogen bonds : bond 0.05945 ( 716) hydrogen bonds : angle 4.16459 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.552 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: symmetry clash REVERT: A 143 LEU cc_start: 0.8895 (mt) cc_final: 0.8627 (mp) REVERT: A 303 TYR cc_start: 0.8687 (m-80) cc_final: 0.8372 (m-10) REVERT: A 441 ASP cc_start: 0.8634 (t70) cc_final: 0.8238 (m-30) REVERT: A 466 ASP cc_start: 0.7447 (p0) cc_final: 0.7238 (t0) REVERT: A 697 PHE cc_start: 0.7268 (t80) cc_final: 0.6938 (t80) REVERT: B 839 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 878 GLU cc_start: 0.8918 (tp30) cc_final: 0.8590 (tp30) REVERT: C 1014 PHE cc_start: 0.8771 (t80) cc_final: 0.8449 (t80) REVERT: C 1077 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6946 (tm130) outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 0.2430 time to fit residues: 40.5289 Evaluate side-chains 92 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1143 LYS Chi-restraints excluded: chain D residue 1464 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN C1161 GLN D1502 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.079104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.062597 restraints weight = 106789.377| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.83 r_work: 0.3214 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9782 Z= 0.168 Angle : 0.514 6.890 13122 Z= 0.289 Chirality : 0.033 0.131 1477 Planarity : 0.003 0.036 1648 Dihedral : 3.982 22.375 1232 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.09 % Allowed : 7.97 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.25), residues: 1140 helix: 1.84 (0.17), residues: 919 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 204 TYR 0.014 0.001 TYR A 559 PHE 0.014 0.001 PHE A 163 HIS 0.006 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9780) covalent geometry : angle 0.51301 (13118) SS BOND : bond 0.00915 ( 2) SS BOND : angle 2.16491 ( 4) hydrogen bonds : bond 0.05356 ( 716) hydrogen bonds : angle 4.02729 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.579 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 303 TYR cc_start: 0.8769 (m-80) cc_final: 0.8406 (m-10) REVERT: A 697 PHE cc_start: 0.7301 (t80) cc_final: 0.6950 (t80) REVERT: B 824 MET cc_start: 0.8343 (ttt) cc_final: 0.8038 (ttp) outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 0.2402 time to fit residues: 31.5571 Evaluate side-chains 86 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain C residue 1077 GLN Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain C residue 1123 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN C1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.079510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063061 restraints weight = 105901.495| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.79 r_work: 0.3230 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9782 Z= 0.122 Angle : 0.472 8.319 13122 Z= 0.261 Chirality : 0.032 0.194 1477 Planarity : 0.003 0.038 1648 Dihedral : 3.861 36.307 1232 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.91 % Allowed : 8.79 % Favored : 90.31 % 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: 2.70 (0.25), residues: 1140 helix: 2.22 (0.17), residues: 914 sheet: None (None), residues: 0 loop : 0.04 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.011 0.001 TYR A 559 PHE 0.013 0.001 PHE A 163 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9780) covalent geometry : angle 0.46589 (13118) SS BOND : bond 0.00551 ( 2) SS BOND : angle 4.46642 ( 4) hydrogen bonds : bond 0.04950 ( 716) hydrogen bonds : angle 3.76278 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 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: symmetry clash REVERT: A 165 LEU cc_start: 0.8722 (tp) cc_final: 0.8359 (tt) REVERT: A 303 TYR cc_start: 0.8734 (m-80) cc_final: 0.8398 (m-10) REVERT: A 697 PHE cc_start: 0.7245 (t80) cc_final: 0.6905 (t80) REVERT: B 824 MET cc_start: 0.8387 (ttt) cc_final: 0.8066 (ttp) REVERT: B 839 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 878 GLU cc_start: 0.8897 (tp30) cc_final: 0.8665 (tp30) REVERT: C 999 MET cc_start: 0.8235 (tpp) cc_final: 0.7955 (tpt) REVERT: D 1515 ASP cc_start: 0.9246 (OUTLIER) cc_final: 0.8898 (m-30) outliers start: 10 outliers final: 3 residues processed: 101 average time/residue: 0.2151 time to fit residues: 31.1096 Evaluate side-chains 86 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain C residue 1123 GLU Chi-restraints excluded: chain D residue 1515 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN C1081 GLN C1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.079078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062528 restraints weight = 106125.641| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.81 r_work: 0.3219 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9782 Z= 0.124 Angle : 0.456 6.201 13122 Z= 0.252 Chirality : 0.031 0.130 1477 Planarity : 0.003 0.033 1648 Dihedral : 3.612 25.540 1232 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.00 % Allowed : 9.06 % Favored : 89.95 % 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: 3.03 (0.25), residues: 1140 helix: 2.48 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.008 0.001 TYR A 559 PHE 0.010 0.001 PHE A 163 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9780) covalent geometry : angle 0.45227 (13118) SS BOND : bond 0.00841 ( 2) SS BOND : angle 3.16551 ( 4) hydrogen bonds : bond 0.04667 ( 716) hydrogen bonds : angle 3.68019 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.545 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: A 303 TYR cc_start: 0.8764 (m-80) cc_final: 0.8461 (m-10) REVERT: A 445 ASN cc_start: 0.8555 (m-40) cc_final: 0.8242 (p0) REVERT: B 824 MET cc_start: 0.8595 (ttt) cc_final: 0.8277 (ttp) REVERT: B 839 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8028 (mm-30) REVERT: B 878 GLU cc_start: 0.8905 (tp30) cc_final: 0.8691 (tp30) REVERT: B 904 GLN cc_start: 0.6253 (tp-100) cc_final: 0.5864 (tp-100) REVERT: C 999 MET cc_start: 0.8253 (tpp) cc_final: 0.7973 (tpt) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 0.2093 time to fit residues: 29.7171 Evaluate side-chains 84 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain C residue 1123 GLU Chi-restraints excluded: chain D residue 1515 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN B 881 GLN C1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.078797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.062294 restraints weight = 107205.517| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.81 r_work: 0.3208 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9782 Z= 0.124 Angle : 0.455 6.270 13122 Z= 0.250 Chirality : 0.031 0.130 1477 Planarity : 0.003 0.030 1648 Dihedral : 3.560 28.937 1232 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.82 % Allowed : 10.42 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.24 (0.25), residues: 1140 helix: 2.64 (0.17), residues: 913 sheet: None (None), residues: 0 loop : 0.03 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.014 0.001 TYR A 421 PHE 0.011 0.001 PHE A 163 HIS 0.004 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9780) covalent geometry : angle 0.45176 (13118) SS BOND : bond 0.00588 ( 2) SS BOND : angle 3.19410 ( 4) hydrogen bonds : bond 0.04549 ( 716) hydrogen bonds : angle 3.62390 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.709 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: A 293 LEU cc_start: 0.9076 (tp) cc_final: 0.8701 (tp) REVERT: A 303 TYR cc_start: 0.8819 (m-80) cc_final: 0.8468 (m-10) REVERT: A 445 ASN cc_start: 0.8613 (m-40) cc_final: 0.8297 (p0) REVERT: A 697 PHE cc_start: 0.7230 (t80) cc_final: 0.6858 (t80) REVERT: B 824 MET cc_start: 0.8607 (ttt) cc_final: 0.8276 (ttp) REVERT: B 904 GLN cc_start: 0.6249 (tp-100) cc_final: 0.5922 (tp-100) REVERT: C 999 MET cc_start: 0.8274 (tpp) cc_final: 0.7975 (tpt) outliers start: 9 outliers final: 5 residues processed: 88 average time/residue: 0.2247 time to fit residues: 28.8502 Evaluate side-chains 78 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain C residue 1179 ASP Chi-restraints excluded: chain D residue 1515 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 26 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN B 856 ASN B 881 GLN C1161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.078681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.062145 restraints weight = 108050.458| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.83 r_work: 0.3203 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9782 Z= 0.120 Angle : 0.446 7.320 13122 Z= 0.245 Chirality : 0.031 0.129 1477 Planarity : 0.003 0.033 1648 Dihedral : 3.452 25.343 1232 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.91 % Allowed : 10.69 % Favored : 88.41 % 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: 3.48 (0.25), residues: 1140 helix: 2.82 (0.17), residues: 912 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.007 0.001 TYR B 887 PHE 0.010 0.001 PHE A 163 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9780) covalent geometry : angle 0.44248 (13118) SS BOND : bond 0.00331 ( 2) SS BOND : angle 3.38361 ( 4) hydrogen bonds : bond 0.04417 ( 716) hydrogen bonds : angle 3.55827 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.539 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 293 LEU cc_start: 0.9125 (tp) cc_final: 0.8747 (tp) REVERT: A 303 TYR cc_start: 0.8845 (m-80) cc_final: 0.8499 (m-10) REVERT: A 445 ASN cc_start: 0.8633 (m-40) cc_final: 0.8298 (p0) REVERT: B 824 MET cc_start: 0.8637 (ttt) cc_final: 0.8313 (ttp) REVERT: B 904 GLN cc_start: 0.6351 (tp-100) cc_final: 0.5902 (tp-100) REVERT: C 999 MET cc_start: 0.8298 (tpp) cc_final: 0.7993 (tpt) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 0.2097 time to fit residues: 27.6157 Evaluate side-chains 83 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain C residue 1123 GLU Chi-restraints excluded: chain C residue 1179 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN A 677 ASN C1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.077851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061321 restraints weight = 108700.576| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.80 r_work: 0.3184 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9782 Z= 0.148 Angle : 0.468 8.114 13122 Z= 0.259 Chirality : 0.032 0.129 1477 Planarity : 0.003 0.031 1648 Dihedral : 3.438 20.371 1232 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.18 % Allowed : 10.51 % Favored : 88.32 % 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: 3.43 (0.25), residues: 1140 helix: 2.80 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 577 TYR 0.010 0.001 TYR B 887 PHE 0.010 0.001 PHE C1021 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9780) covalent geometry : angle 0.46434 (13118) SS BOND : bond 0.00377 ( 2) SS BOND : angle 3.58890 ( 4) hydrogen bonds : bond 0.04480 ( 716) hydrogen bonds : angle 3.64233 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.571 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 293 LEU cc_start: 0.9166 (tp) cc_final: 0.8810 (tp) REVERT: A 303 TYR cc_start: 0.8890 (m-80) cc_final: 0.8559 (m-10) REVERT: A 445 ASN cc_start: 0.8692 (m-40) cc_final: 0.8355 (p0) REVERT: A 697 PHE cc_start: 0.7158 (t80) cc_final: 0.6808 (t80) REVERT: B 824 MET cc_start: 0.8712 (ttt) cc_final: 0.8391 (ttp) REVERT: B 904 GLN cc_start: 0.6592 (tp-100) cc_final: 0.6127 (tp-100) REVERT: C 999 MET cc_start: 0.8332 (tpp) cc_final: 0.8024 (tpt) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.2094 time to fit residues: 27.1654 Evaluate side-chains 86 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain C residue 1123 GLU Chi-restraints excluded: chain D residue 1515 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN C1161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.078471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061956 restraints weight = 106638.939| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.81 r_work: 0.3203 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9782 Z= 0.110 Angle : 0.451 8.591 13122 Z= 0.247 Chirality : 0.031 0.137 1477 Planarity : 0.003 0.036 1648 Dihedral : 3.464 25.088 1232 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.82 % Allowed : 11.05 % Favored : 88.13 % 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: 3.62 (0.25), residues: 1140 helix: 2.94 (0.17), residues: 910 sheet: None (None), residues: 0 loop : 0.04 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.007 0.001 TYR A 215 PHE 0.014 0.001 PHE A 525 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9780) covalent geometry : angle 0.44562 (13118) SS BOND : bond 0.00415 ( 2) SS BOND : angle 3.98492 ( 4) hydrogen bonds : bond 0.04401 ( 716) hydrogen bonds : angle 3.51643 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.550 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: A 293 LEU cc_start: 0.9148 (tp) cc_final: 0.8784 (tp) REVERT: A 303 TYR cc_start: 0.8881 (m-80) cc_final: 0.8547 (m-10) REVERT: A 445 ASN cc_start: 0.8682 (m-40) cc_final: 0.8344 (p0) REVERT: A 697 PHE cc_start: 0.7097 (t80) cc_final: 0.6769 (t80) REVERT: B 824 MET cc_start: 0.8709 (ttt) cc_final: 0.8386 (ttp) REVERT: B 841 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: B 904 GLN cc_start: 0.6524 (tp-100) cc_final: 0.6067 (tp-100) REVERT: C 999 MET cc_start: 0.8334 (tpp) cc_final: 0.8033 (tpt) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.1962 time to fit residues: 24.5754 Evaluate side-chains 83 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 677 ASN Chi-restraints excluded: chain B residue 841 GLU Chi-restraints excluded: chain C residue 1123 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 0.0170 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN A 677 ASN C1161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.078764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062169 restraints weight = 107816.855| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.86 r_work: 0.3203 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9782 Z= 0.106 Angle : 0.458 9.582 13122 Z= 0.246 Chirality : 0.031 0.129 1477 Planarity : 0.002 0.032 1648 Dihedral : 3.399 23.941 1232 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.72 % Allowed : 11.23 % Favored : 88.04 % 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: 3.73 (0.25), residues: 1140 helix: 3.02 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 0.10 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.008 0.001 TYR B 887 PHE 0.009 0.001 PHE C1021 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9780) covalent geometry : angle 0.45371 (13118) SS BOND : bond 0.00328 ( 2) SS BOND : angle 3.72053 ( 4) hydrogen bonds : bond 0.04306 ( 716) hydrogen bonds : angle 3.48762 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.577 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: A 293 LEU cc_start: 0.9153 (tp) cc_final: 0.8782 (tp) REVERT: A 303 TYR cc_start: 0.8876 (m-80) cc_final: 0.8544 (m-10) REVERT: A 445 ASN cc_start: 0.8690 (m-40) cc_final: 0.8344 (p0) REVERT: B 824 MET cc_start: 0.8700 (ttt) cc_final: 0.8372 (ttp) REVERT: B 841 GLU cc_start: 0.8300 (tt0) cc_final: 0.8033 (tm-30) REVERT: B 904 GLN cc_start: 0.6480 (tp-100) cc_final: 0.6076 (tp-100) REVERT: C 999 MET cc_start: 0.8342 (tpp) cc_final: 0.8040 (tpt) REVERT: C 1161 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7379 (tm-30) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.2159 time to fit residues: 26.8114 Evaluate side-chains 83 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 523 ASN Chi-restraints excluded: chain C residue 1161 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.078721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062138 restraints weight = 107747.381| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.86 r_work: 0.3204 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 9782 Z= 0.243 Angle : 1.055 59.199 13122 Z= 0.664 Chirality : 0.034 0.522 1477 Planarity : 0.003 0.055 1648 Dihedral : 3.399 23.838 1232 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.36 % Allowed : 11.41 % Favored : 88.22 % Cbeta Deviations : 0.18 % 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: 3.71 (0.25), residues: 1140 helix: 3.00 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 0.10 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.007 0.001 TYR B 865 PHE 0.010 0.001 PHE C1021 HIS 0.005 0.001 HIS B 814 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9780) covalent geometry : angle 1.05382 (13118) SS BOND : bond 0.00510 ( 2) SS BOND : angle 3.52656 ( 4) hydrogen bonds : bond 0.04326 ( 716) hydrogen bonds : angle 3.48139 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.15 seconds wall clock time: 71 minutes 29.01 seconds (4289.01 seconds total)