Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 05:15:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbc_11150/04_2023/6zbc_11150.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.044 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 None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: 8.74, per 1000 atoms: 0.45 Number of scatterers: 19534 At special positions: 0 Unit cell: (105.154, 136.271, 140.563, 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=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=1.96 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 16.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 49 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.618A 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: 4.070A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.213A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.525A 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: 4.286A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.921A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.512A 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: 3.632A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.144A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.911A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 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: 3.735A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.989A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.741A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.508A pdb=" N PHE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.952A 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: 3.889A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.612A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.289A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.633A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.664A 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: 3.854A pdb=" N VAL B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.705A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.965A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.001A 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: 3.777A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1025 removed outlier: 3.615A 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: 3.554A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.524A pdb=" N TYR C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1108 No H-bonds generated for 'chain 'C' and resid 1106 through 1108' Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.705A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C1130 " --> pdb=" O ASN C1126 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.078A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.641A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.544A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.540A 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: 3.627A 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: 3.643A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.632A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.700A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.561A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 717 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: 7.55 Time building geometry restraints manager: 17.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9900 1.03 - 1.23: 26 1.23 - 1.42: 3885 1.42 - 1.61: 5839 1.61 - 1.81: 32 Bond restraints: 19682 Sorted by residual: bond pdb=" N VAL B 819 " pdb=" CA VAL B 819 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.19e-02 7.06e+03 1.22e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N ILE D1346 " pdb=" CA ILE D1346 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.21e-02 6.83e+03 1.17e+01 bond pdb=" N VAL D1345 " pdb=" CA VAL D1345 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N ILE C1029 " pdb=" CA ILE C1029 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.19e-02 7.06e+03 1.01e+01 ... (remaining 19677 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.40: 196 105.40 - 112.01: 23139 112.01 - 118.61: 4705 118.61 - 125.22: 7592 125.22 - 131.83: 222 Bond angle restraints: 35854 Sorted by residual: angle pdb=" N VAL C1022 " pdb=" CA VAL C1022 " pdb=" C VAL C1022 " ideal model delta sigma weight residual 110.62 117.29 -6.67 1.02e+00 9.61e-01 4.28e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.07 6.21 1.09e+00 8.42e-01 3.25e+01 angle pdb=" N ILE A 362 " pdb=" CA ILE A 362 " pdb=" C ILE A 362 " ideal model delta sigma weight residual 110.62 104.81 5.81 1.02e+00 9.61e-01 3.24e+01 angle pdb=" N PHE C1014 " pdb=" CA PHE C1014 " pdb=" C PHE C1014 " ideal model delta sigma weight residual 111.28 105.24 6.04 1.09e+00 8.42e-01 3.07e+01 angle pdb=" N LEU C1099 " pdb=" CA LEU C1099 " pdb=" C LEU C1099 " ideal model delta sigma weight residual 111.28 105.41 5.87 1.09e+00 8.42e-01 2.90e+01 ... (remaining 35849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7262 17.87 - 35.74: 493 35.74 - 53.61: 94 53.61 - 71.49: 27 71.49 - 89.36: 13 Dihedral angle restraints: 7889 sinusoidal: 3850 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 93.00 141.63 -48.63 1 1.00e+01 1.00e-02 3.25e+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 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLU B 894 " pdb=" C GLU B 894 " pdb=" N ASN B 895 " pdb=" CA ASN B 895 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1167 0.056 - 0.113: 243 0.113 - 0.169: 53 0.169 - 0.226: 12 0.226 - 0.282: 2 Chirality restraints: 1477 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 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 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 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA LEU C1106 " pdb=" N LEU C1106 " pdb=" C LEU C1106 " pdb=" CB LEU C1106 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1474 not shown) Planarity restraints: 2773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLN A 217 " -0.072 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C1099 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LEU C1099 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU C1099 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C1100 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 256 " 0.009 2.00e-02 2.50e+03 1.73e-02 8.94e+00 pdb=" CG TYR A 256 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 256 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 256 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 256 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 256 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 256 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 256 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR A 256 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 256 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 TYR A 256 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 256 " -0.009 2.00e-02 2.50e+03 ... (remaining 2770 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1477 2.26 - 2.84: 45725 2.84 - 3.43: 48968 3.43 - 4.01: 62976 4.01 - 4.60: 101047 Nonbonded interactions: 260193 Sorted by model distance: nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.670 1.850 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.692 1.850 nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.699 1.850 nonbonded pdb=" HG1 THR A 21 " pdb=" O PRO A 428 " model vdw 1.700 1.850 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.703 1.850 ... (remaining 260188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.270 Extract box with map and model: 6.710 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 62.090 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.007 0.063 9780 Z= 0.462 Angle : 1.019 8.420 13118 Z= 0.684 Chirality : 0.052 0.282 1477 Planarity : 0.005 0.041 1648 Dihedral : 13.799 89.357 3844 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1140 helix: -0.35 (0.16), residues: 903 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 237 *********************** 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 157 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.962 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 outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.6204 time to fit residues: 129.6699 Evaluate side-chains 73 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN C1224 ASN D1419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9780 Z= 0.177 Angle : 0.554 5.865 13118 Z= 0.304 Chirality : 0.034 0.145 1477 Planarity : 0.003 0.036 1648 Dihedral : 4.287 23.309 1232 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1140 helix: 1.09 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -0.22 (0.41), residues: 222 *********************** 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 77 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.654 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 outliers start: 8 outliers final: 6 residues processed: 74 average time/residue: 0.5198 time to fit residues: 55.1276 Evaluate side-chains 58 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3395 time to fit residues: 5.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 856 ASN C1224 ASN D1400 HIS D1502 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9780 Z= 0.235 Angle : 0.516 6.803 13118 Z= 0.283 Chirality : 0.033 0.132 1477 Planarity : 0.003 0.033 1648 Dihedral : 3.999 30.111 1232 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1140 helix: 1.78 (0.17), residues: 915 sheet: None (None), residues: 0 loop : -0.14 (0.42), residues: 225 *********************** 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 55 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.757 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 outliers start: 2 outliers final: 1 residues processed: 54 average time/residue: 0.5310 time to fit residues: 42.0875 Evaluate side-chains 47 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2224 time to fit residues: 2.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9780 Z= 0.142 Angle : 0.454 5.587 13118 Z= 0.246 Chirality : 0.032 0.133 1477 Planarity : 0.002 0.031 1648 Dihedral : 3.804 29.220 1232 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.25), residues: 1140 helix: 2.21 (0.17), residues: 915 sheet: None (None), residues: 0 loop : 0.09 (0.42), residues: 225 *********************** 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 53 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.817 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 outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.5224 time to fit residues: 39.0784 Evaluate side-chains 48 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2121 time to fit residues: 2.9619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN C1097 ASN C1183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9780 Z= 0.194 Angle : 0.456 5.450 13118 Z= 0.251 Chirality : 0.032 0.162 1477 Planarity : 0.002 0.030 1648 Dihedral : 3.633 21.443 1232 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.25), residues: 1140 helix: 2.48 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.17 (0.42), residues: 224 *********************** 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 51 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.789 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 outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.5310 time to fit residues: 37.3791 Evaluate side-chains 45 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2116 time to fit residues: 3.7652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9780 Z= 0.175 Angle : 0.442 5.207 13118 Z= 0.242 Chirality : 0.032 0.132 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.553 27.101 1232 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.25), residues: 1140 helix: 2.71 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.23 (0.42), residues: 224 *********************** 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 50 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 1.769 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 outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.5377 time to fit residues: 39.5093 Evaluate side-chains 43 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 9780 Z= 0.164 Angle : 0.431 5.083 13118 Z= 0.236 Chirality : 0.031 0.132 1477 Planarity : 0.002 0.029 1648 Dihedral : 3.433 14.064 1232 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.25), residues: 1140 helix: 2.86 (0.17), residues: 916 sheet: None (None), residues: 0 loop : 0.27 (0.42), residues: 224 *********************** 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 52 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 1.763 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 outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.5957 time to fit residues: 43.0965 Evaluate side-chains 45 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2374 time to fit residues: 3.4685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 9780 Z= 0.162 Angle : 0.430 5.100 13118 Z= 0.234 Chirality : 0.031 0.131 1477 Planarity : 0.002 0.028 1648 Dihedral : 3.418 24.109 1232 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.25), residues: 1140 helix: 2.98 (0.17), residues: 917 sheet: None (None), residues: 0 loop : 0.31 (0.43), residues: 223 *********************** 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 47 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.749 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 outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.5511 time to fit residues: 36.7982 Evaluate side-chains 44 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4487 time to fit residues: 2.7058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 9780 Z= 0.267 Angle : 0.478 4.863 13118 Z= 0.266 Chirality : 0.033 0.163 1477 Planarity : 0.003 0.027 1648 Dihedral : 3.494 16.858 1232 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.25), residues: 1140 helix: 2.84 (0.16), residues: 911 sheet: None (None), residues: 0 loop : 0.08 (0.42), residues: 229 *********************** 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 46 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 1.637 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 outliers start: 4 outliers final: 2 residues processed: 43 average time/residue: 0.5253 time to fit residues: 33.1386 Evaluate side-chains 44 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2225 time to fit residues: 2.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 9780 Z= 0.150 Angle : 0.435 4.875 13118 Z= 0.236 Chirality : 0.031 0.135 1477 Planarity : 0.002 0.028 1648 Dihedral : 3.483 31.111 1232 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.25), residues: 1140 helix: 3.06 (0.17), residues: 917 sheet: None (None), residues: 0 loop : 0.31 (0.43), residues: 223 ********************** 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 45 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5863 time to fit residues: 37.7308 Evaluate side-chains 42 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.072609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056574 restraints weight = 94332.628| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.54 r_work: 0.3037 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 9780 Z= 0.145 Angle : 0.426 4.898 13118 Z= 0.231 Chirality : 0.031 0.131 1477 Planarity : 0.002 0.031 1648 Dihedral : 3.364 19.529 1232 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.25), residues: 1140 helix: 3.19 (0.17), residues: 917 sheet: None (None), residues: 0 loop : 0.36 (0.43), residues: 223 =============================================================================== Job complete usr+sys time: 3766.62 seconds wall clock time: 68 minutes 16.33 seconds (4096.33 seconds total)