Starting phenix.real_space_refine on Thu Jul 2 10:19:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wit_32535/07_2026/7wit_32535.map" } resolution = 3.21 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= 0.007 sd= 0.105 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 P 3 5.49 5 S 38 5.16 5 C 5222 2.51 5 N 1396 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8109 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8055 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 239} Link IDs: {'PTRANS': 35, 'TRANS': 1097} Chain breaks: 8 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1072 Unresolved non-hydrogen dihedrals: 686 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'PHE:plan': 13, 'ASP:plan': 26, 'GLN:plan1': 21, 'ARG:plan': 20, 'GLU:plan': 20, 'ASN:plan1': 6, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 468 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'9I0': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.02, per 1000 atoms: 0.25 Number of scatterers: 8109 At special positions: 0 Unit cell: (97.185, 133.76, 77.33, 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 38 16.00 P 3 15.00 O 1450 8.00 N 1396 7.00 C 5222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.71 Conformation dependent library (CDL) restraints added in 500.7 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 70.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.223A pdb=" N ALA A 235 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 236 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.592A pdb=" N TRP A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 314 removed outlier: 3.679A pdb=" N LEU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 354 through 400 removed outlier: 3.566A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 removed outlier: 3.940A pdb=" N CYS A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 436 through 457 Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 457 through 470 removed outlier: 4.022A pdb=" N LEU A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 505 removed outlier: 3.874A pdb=" N HIS A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 514 through 565 removed outlier: 3.927A pdb=" N ALA A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 543 " --> pdb=" O TYR A 539 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 572 through 614 removed outlier: 3.681A pdb=" N ILE A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 588 " --> pdb=" O HIS A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.865A pdb=" N SER A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER A 595 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.541A pdb=" N LEU A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 790 Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 808 through 815 removed outlier: 3.737A pdb=" N ILE A 814 " --> pdb=" O PRO A 810 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 828 removed outlier: 3.508A pdb=" N GLY A 827 " --> pdb=" O GLY A 824 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 828 " --> pdb=" O GLU A 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 824 through 828' Processing helix chain 'A' and resid 831 through 846 removed outlier: 3.516A pdb=" N ARG A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 846 " --> pdb=" O ARG A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 890 through 894 removed outlier: 4.154A pdb=" N TYR A 893 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 921 Processing helix chain 'A' and resid 998 through 1007 removed outlier: 3.668A pdb=" N SER A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1024 Processing helix chain 'A' and resid 1026 through 1039 removed outlier: 3.941A pdb=" N ASP A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1106 removed outlier: 3.718A pdb=" N ALA A1065 " --> pdb=" O GLN A1061 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A1086 " --> pdb=" O THR A1082 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.852A pdb=" N PHE A1113 " --> pdb=" O PRO A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 removed outlier: 3.766A pdb=" N ILE A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1135 Processing helix chain 'A' and resid 1135 through 1161 removed outlier: 3.554A pdb=" N SER A1158 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1166 Processing helix chain 'A' and resid 1167 through 1210 removed outlier: 3.618A pdb=" N ASP A1188 " --> pdb=" O VAL A1184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1198 " --> pdb=" O ASP A1194 " (cutoff:3.500A) Proline residue: A1199 - end of helix Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1219 through 1274 removed outlier: 3.536A pdb=" N LEU A1228 " --> pdb=" O GLN A1224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A1229 " --> pdb=" O GLN A1225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A1242 " --> pdb=" O SER A1238 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A1261 " --> pdb=" O ALA A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1289 removed outlier: 3.577A pdb=" N TYR A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1309 Processing helix chain 'A' and resid 1309 through 1319 Processing helix chain 'A' and resid 1384 through 1392 removed outlier: 3.748A pdb=" N PHE A1388 " --> pdb=" O GLY A1384 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A1389 " --> pdb=" O LYS A1385 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A1390 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A1392 " --> pdb=" O PHE A1388 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1419 Processing helix chain 'A' and resid 1420 through 1422 No H-bonds generated for 'chain 'A' and resid 1420 through 1422' Processing helix chain 'A' and resid 1436 through 1441 removed outlier: 3.509A pdb=" N ASP A1441 " --> pdb=" O ARG A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1458 Processing helix chain 'A' and resid 1460 through 1467 Processing helix chain 'A' and resid 1483 through 1499 removed outlier: 3.780A pdb=" N ARG A1498 " --> pdb=" O ARG A1494 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A1499 " --> pdb=" O ALA A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1527 Processing helix chain 'A' and resid 1562 through 1570 removed outlier: 3.738A pdb=" N SER A1568 " --> pdb=" O GLU A1564 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 697 removed outlier: 4.280A pdb=" N GLY A 684 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER A 734 " --> pdb=" O GLY A 684 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE A 686 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LYS A 732 " --> pdb=" O PHE A 686 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 770 through 773 removed outlier: 6.609A pdb=" N MET A 710 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N MET A 903 " --> pdb=" O MET A 710 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 712 " --> pdb=" O MET A 903 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 900 " --> pdb=" O GLU A 911 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU A 911 " --> pdb=" O ILE A 900 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ALA A 902 " --> pdb=" O GLN A 909 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1367 through 1369 removed outlier: 3.808A pdb=" N ALA A1367 " --> pdb=" O ILE A1347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 3.707A pdb=" N LEU A1362 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1503 through 1506 574 hydrogen bonds defined for protein. 1686 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: 1.55 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2156 1.33 - 1.45: 1353 1.45 - 1.57: 4689 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 8262 Sorted by residual: bond pdb=" C12 9I0 A2002 " pdb=" O1 9I0 A2002 " ideal model delta sigma weight residual 1.250 1.328 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C10 9I0 A2002 " pdb=" C12 9I0 A2002 " ideal model delta sigma weight residual 1.545 1.493 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 9I0 A2002 " pdb=" O2 9I0 A2002 " ideal model delta sigma weight residual 1.246 1.218 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C 9I0 A2002 " pdb=" C1 9I0 A2002 " ideal model delta sigma weight residual 1.541 1.515 0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" N 9I0 A2002 " pdb=" C8 9I0 A2002 " ideal model delta sigma weight residual 1.346 1.321 0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 8257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11030 1.48 - 2.96: 206 2.96 - 4.44: 44 4.44 - 5.92: 14 5.92 - 7.40: 4 Bond angle restraints: 11298 Sorted by residual: angle pdb=" N VAL A1028 " pdb=" CA VAL A1028 " pdb=" C VAL A1028 " ideal model delta sigma weight residual 111.81 108.62 3.19 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N LYS A1445 " pdb=" CA LYS A1445 " pdb=" C LYS A1445 " ideal model delta sigma weight residual 114.31 110.43 3.88 1.29e+00 6.01e-01 9.04e+00 angle pdb=" O1 9I0 A2002 " pdb=" C12 9I0 A2002 " pdb=" O2 9I0 A2002 " ideal model delta sigma weight residual 126.72 119.32 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" C ILE A1105 " pdb=" CA ILE A1105 " pdb=" CB ILE A1105 " ideal model delta sigma weight residual 112.26 108.76 3.50 1.62e+00 3.81e-01 4.67e+00 angle pdb=" N MET A1025 " pdb=" CA MET A1025 " pdb=" C MET A1025 " ideal model delta sigma weight residual 113.28 110.68 2.60 1.22e+00 6.72e-01 4.53e+00 ... (remaining 11293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.58: 4336 11.58 - 23.16: 378 23.16 - 34.74: 104 34.74 - 46.32: 33 46.32 - 57.90: 18 Dihedral angle restraints: 4869 sinusoidal: 1571 harmonic: 3298 Sorted by residual: dihedral pdb=" CA TYR A 539 " pdb=" C TYR A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 162.16 17.84 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A1024 " pdb=" C HIS A1024 " pdb=" N MET A1025 " pdb=" CA MET A1025 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG A 370 " pdb=" C ARG A 370 " pdb=" N THR A 371 " pdb=" CA THR A 371 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 791 0.030 - 0.059: 450 0.059 - 0.089: 96 0.089 - 0.119: 58 0.119 - 0.148: 6 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA GLN A 219 " pdb=" N GLN A 219 " pdb=" C GLN A 219 " pdb=" CB GLN A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ARG A1531 " pdb=" N ARG A1531 " pdb=" C ARG A1531 " pdb=" CB ARG A1531 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA THR A 588 " pdb=" N THR A 588 " pdb=" C THR A 588 " pdb=" CB THR A 588 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1398 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 9I0 A2002 " -0.001 2.00e-02 2.50e+03 5.61e-02 4.73e+01 pdb=" O 9I0 A2002 " 0.069 2.00e-02 2.50e+03 pdb=" C2 9I0 A2002 " -0.068 2.00e-02 2.50e+03 pdb=" C3 9I0 A2002 " 0.067 2.00e-02 2.50e+03 pdb=" C8 9I0 A2002 " 0.005 2.00e-02 2.50e+03 pdb=" C9 9I0 A2002 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 316 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 317 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 588 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 589 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.017 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2131 2.80 - 3.32: 8208 3.32 - 3.85: 12596 3.85 - 4.37: 14816 4.37 - 4.90: 25510 Nonbonded interactions: 63261 Sorted by model distance: nonbonded pdb=" O ALA A 554 " pdb=" OG1 THR A 558 " model vdw 2.271 3.040 nonbonded pdb=" O THR A1161 " pdb=" OG1 THR A1161 " model vdw 2.285 3.040 nonbonded pdb=" O ASP A 424 " pdb=" OG SER A 606 " model vdw 2.299 3.040 nonbonded pdb=" O ASP A 861 " pdb=" OG SER A 865 " model vdw 2.328 3.040 nonbonded pdb=" OD2 ASP A1031 " pdb=" OH TYR A1287 " model vdw 2.330 3.040 ... (remaining 63256 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: 1.090 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.550 Find NCS groups from input model: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8262 Z= 0.207 Angle : 0.565 7.398 11298 Z= 0.299 Chirality : 0.040 0.148 1401 Planarity : 0.004 0.056 1407 Dihedral : 11.082 57.904 2723 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.11 % Allowed : 7.04 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1115 helix: -0.59 (0.18), residues: 750 sheet: -0.30 (0.70), residues: 68 loop : -0.19 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1314 TYR 0.011 0.001 TYR A 230 PHE 0.010 0.001 PHE A1217 TRP 0.011 0.001 TRP A 739 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 ( 8262) covalent geometry : angle 0.56518 / 0.30 (11298) hydrogen bonds : bond 0.26183 / 17.55 ( 574) hydrogen bonds : angle 8.33791 / 5.97 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7085 (mpt180) REVERT: A 469 LEU cc_start: 0.8098 (tt) cc_final: 0.7622 (mp) REVERT: A 781 ASN cc_start: 0.8563 (t0) cc_final: 0.8345 (m-40) REVERT: A 903 MET cc_start: 0.7219 (mmm) cc_final: 0.6015 (mmm) REVERT: A 1018 PHE cc_start: 0.7033 (t80) cc_final: 0.6647 (t80) outliers start: 23 outliers final: 4 residues processed: 150 average time/residue: 0.1028 time to fit residues: 20.6568 Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 1350 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 GLN A1296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112436 restraints weight = 12678.742| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.62 r_work: 0.3437 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8262 Z= 0.133 Angle : 0.541 8.110 11298 Z= 0.280 Chirality : 0.040 0.144 1401 Planarity : 0.004 0.035 1407 Dihedral : 5.816 58.647 1237 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.71 % Allowed : 12.04 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.25), residues: 1115 helix: 1.12 (0.18), residues: 767 sheet: -0.30 (0.68), residues: 69 loop : -0.20 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 878 TYR 0.014 0.001 TYR A 230 PHE 0.028 0.001 PHE A 738 TRP 0.010 0.001 TRP A 430 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 8262) covalent geometry : angle 0.54130 / 0.28 (11298) hydrogen bonds : bond 0.05018 / 3.43 ( 574) hydrogen bonds : angle 4.39650 / 3.17 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7065 (mpt180) REVERT: A 469 LEU cc_start: 0.7916 (tt) cc_final: 0.7560 (mp) REVERT: A 592 LEU cc_start: 0.8079 (tp) cc_final: 0.7636 (mp) REVERT: A 721 SER cc_start: 0.8973 (t) cc_final: 0.8574 (m) REVERT: A 836 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: A 903 MET cc_start: 0.7213 (mmm) cc_final: 0.5993 (mmm) REVERT: A 1191 GLN cc_start: 0.6993 (mt0) cc_final: 0.6673 (mp10) REVERT: A 1253 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6826 (mt-10) REVERT: A 1287 TYR cc_start: 0.8701 (m-80) cc_final: 0.8330 (m-80) REVERT: A 1290 MET cc_start: 0.8220 (tpp) cc_final: 0.7985 (mmt) outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.0864 time to fit residues: 14.1339 Evaluate side-chains 89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1079 CYS Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1319 LEU Chi-restraints excluded: chain A residue 1350 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 GLN A1296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117349 restraints weight = 12654.991| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.68 r_work: 0.3438 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8262 Z= 0.127 Angle : 0.518 6.616 11298 Z= 0.262 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.034 1407 Dihedral : 5.395 58.547 1236 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.30 % Allowed : 14.34 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.26), residues: 1115 helix: 1.70 (0.19), residues: 769 sheet: -0.30 (0.67), residues: 69 loop : -0.25 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 878 TYR 0.011 0.001 TYR A 230 PHE 0.019 0.001 PHE A 738 TRP 0.009 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8262) covalent geometry : angle 0.51782 / 0.26 (11298) hydrogen bonds : bond 0.04355 / 2.98 ( 574) hydrogen bonds : angle 3.97828 / 2.87 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7033 (mpt180) REVERT: A 469 LEU cc_start: 0.7995 (tt) cc_final: 0.7628 (mp) REVERT: A 494 GLU cc_start: 0.8099 (tp30) cc_final: 0.7878 (tp30) REVERT: A 592 LEU cc_start: 0.8194 (tp) cc_final: 0.7691 (mp) REVERT: A 721 SER cc_start: 0.9011 (t) cc_final: 0.8734 (m) REVERT: A 836 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8004 (tm-30) REVERT: A 1191 GLN cc_start: 0.6822 (mt0) cc_final: 0.6554 (mp10) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.0779 time to fit residues: 10.4298 Evaluate side-chains 85 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1423 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.155993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116675 restraints weight = 12623.149| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.67 r_work: 0.3439 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8262 Z= 0.126 Angle : 0.502 6.098 11298 Z= 0.252 Chirality : 0.039 0.153 1401 Planarity : 0.003 0.033 1407 Dihedral : 5.285 59.008 1235 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.98 % Allowed : 15.29 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.26), residues: 1115 helix: 1.97 (0.19), residues: 769 sheet: -0.13 (0.67), residues: 70 loop : -0.30 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 878 TYR 0.010 0.001 TYR A 378 PHE 0.022 0.001 PHE A 738 TRP 0.008 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8262) covalent geometry : angle 0.50219 / 0.25 (11298) hydrogen bonds : bond 0.04030 / 2.76 ( 574) hydrogen bonds : angle 3.84079 / 2.78 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6978 (mpt180) REVERT: A 469 LEU cc_start: 0.7981 (tt) cc_final: 0.7603 (mp) REVERT: A 485 GLN cc_start: 0.7984 (tt0) cc_final: 0.7403 (tm-30) REVERT: A 494 GLU cc_start: 0.8175 (tp30) cc_final: 0.7947 (tp30) REVERT: A 592 LEU cc_start: 0.8160 (tp) cc_final: 0.7756 (mp) REVERT: A 721 SER cc_start: 0.8865 (t) cc_final: 0.8518 (m) REVERT: A 836 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8255 (tm130) REVERT: A 1191 GLN cc_start: 0.6815 (mt0) cc_final: 0.6525 (mp10) REVERT: A 1206 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7503 (mp0) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.0699 time to fit residues: 11.1321 Evaluate side-chains 93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 0.0870 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118072 restraints weight = 12500.176| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.65 r_work: 0.3460 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.110 Angle : 0.492 6.626 11298 Z= 0.244 Chirality : 0.038 0.139 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.070 59.520 1233 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.84 % Allowed : 17.05 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.26), residues: 1115 helix: 2.18 (0.19), residues: 769 sheet: -0.05 (0.68), residues: 70 loop : -0.30 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1111 TYR 0.009 0.001 TYR A 378 PHE 0.016 0.001 PHE A 738 TRP 0.006 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8262) covalent geometry : angle 0.49153 / 0.24 (11298) hydrogen bonds : bond 0.03771 / 2.56 ( 574) hydrogen bonds : angle 3.71347 / 2.68 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 469 LEU cc_start: 0.8073 (tt) cc_final: 0.7762 (mp) REVERT: A 485 GLN cc_start: 0.8002 (tt0) cc_final: 0.7349 (tm-30) REVERT: A 592 LEU cc_start: 0.8157 (tp) cc_final: 0.7751 (mp) REVERT: A 721 SER cc_start: 0.8872 (t) cc_final: 0.8552 (m) REVERT: A 1014 SER cc_start: 0.8707 (t) cc_final: 0.8036 (p) REVERT: A 1038 THR cc_start: 0.8368 (p) cc_final: 0.8150 (p) REVERT: A 1191 GLN cc_start: 0.6637 (mt0) cc_final: 0.6376 (mp10) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.0753 time to fit residues: 11.2560 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 96 optimal weight: 0.4980 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.159403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119399 restraints weight = 12354.586| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.68 r_work: 0.3481 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8262 Z= 0.097 Angle : 0.468 7.116 11298 Z= 0.233 Chirality : 0.038 0.139 1401 Planarity : 0.003 0.031 1407 Dihedral : 4.653 57.768 1229 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 17.05 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.26), residues: 1115 helix: 2.41 (0.19), residues: 769 sheet: -0.06 (0.67), residues: 70 loop : -0.32 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1111 TYR 0.008 0.001 TYR A 845 PHE 0.014 0.001 PHE A 738 TRP 0.007 0.001 TRP A 430 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8262) covalent geometry : angle 0.46801 / 0.23 (11298) hydrogen bonds : bond 0.03501 / 2.38 ( 574) hydrogen bonds : angle 3.58231 / 2.59 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6986 (mpt180) REVERT: A 469 LEU cc_start: 0.8040 (tt) cc_final: 0.7754 (mp) REVERT: A 485 GLN cc_start: 0.7996 (tt0) cc_final: 0.7347 (tm-30) REVERT: A 592 LEU cc_start: 0.8348 (tp) cc_final: 0.7960 (mp) REVERT: A 721 SER cc_start: 0.8813 (t) cc_final: 0.8523 (m) REVERT: A 1014 SER cc_start: 0.8713 (t) cc_final: 0.8066 (p) REVERT: A 1038 THR cc_start: 0.8374 (p) cc_final: 0.8150 (p) REVERT: A 1191 GLN cc_start: 0.6549 (mt0) cc_final: 0.6317 (mp10) outliers start: 20 outliers final: 16 residues processed: 105 average time/residue: 0.0837 time to fit residues: 12.6525 Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 51 optimal weight: 0.0670 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.155633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.117482 restraints weight = 12223.520| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.40 r_work: 0.3534 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8262 Z= 0.097 Angle : 0.478 9.476 11298 Z= 0.235 Chirality : 0.038 0.158 1401 Planarity : 0.003 0.047 1407 Dihedral : 4.563 57.670 1229 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.11 % Allowed : 17.46 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.26), residues: 1115 helix: 2.49 (0.19), residues: 770 sheet: -0.13 (0.68), residues: 68 loop : -0.22 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 878 TYR 0.008 0.001 TYR A 396 PHE 0.013 0.001 PHE A 738 TRP 0.006 0.001 TRP A1247 HIS 0.002 0.000 HIS A1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 ( 8262) covalent geometry : angle 0.47791 / 0.23 (11298) hydrogen bonds : bond 0.03422 / 2.34 ( 574) hydrogen bonds : angle 3.56939 / 2.58 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7146 (mpt180) REVERT: A 469 LEU cc_start: 0.8029 (tt) cc_final: 0.7790 (mp) REVERT: A 485 GLN cc_start: 0.8185 (tt0) cc_final: 0.7611 (tm-30) REVERT: A 592 LEU cc_start: 0.8384 (tp) cc_final: 0.8007 (mp) REVERT: A 721 SER cc_start: 0.8897 (t) cc_final: 0.8658 (m) REVERT: A 1014 SER cc_start: 0.8819 (t) cc_final: 0.8239 (p) REVERT: A 1191 GLN cc_start: 0.6762 (mt0) cc_final: 0.6550 (mp10) REVERT: A 1206 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7115 (mp0) outliers start: 23 outliers final: 16 residues processed: 102 average time/residue: 0.0700 time to fit residues: 10.5037 Evaluate side-chains 98 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 102 optimal weight: 0.0030 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.154829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116802 restraints weight = 12187.975| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.39 r_work: 0.3526 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8262 Z= 0.103 Angle : 0.478 9.308 11298 Z= 0.234 Chirality : 0.038 0.151 1401 Planarity : 0.003 0.039 1407 Dihedral : 4.584 58.462 1229 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.71 % Allowed : 18.13 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.26), residues: 1115 helix: 2.50 (0.19), residues: 770 sheet: -0.16 (0.68), residues: 68 loop : -0.17 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 878 TYR 0.008 0.001 TYR A 845 PHE 0.013 0.001 PHE A 738 TRP 0.006 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8262) covalent geometry : angle 0.47755 / 0.23 (11298) hydrogen bonds : bond 0.03431 / 2.34 ( 574) hydrogen bonds : angle 3.54438 / 2.56 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7143 (mpt180) REVERT: A 469 LEU cc_start: 0.8054 (tt) cc_final: 0.7801 (mp) REVERT: A 485 GLN cc_start: 0.8212 (tt0) cc_final: 0.7653 (tm-30) REVERT: A 592 LEU cc_start: 0.8422 (tp) cc_final: 0.8030 (mp) REVERT: A 721 SER cc_start: 0.8894 (t) cc_final: 0.8630 (m) REVERT: A 730 MET cc_start: 0.8360 (mmm) cc_final: 0.7814 (mtt) REVERT: A 849 ASN cc_start: 0.7476 (m-40) cc_final: 0.7069 (t0) REVERT: A 1014 SER cc_start: 0.8802 (t) cc_final: 0.8220 (p) REVERT: A 1191 GLN cc_start: 0.6777 (mt0) cc_final: 0.6446 (mp10) REVERT: A 1206 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7079 (mp0) outliers start: 20 outliers final: 17 residues processed: 100 average time/residue: 0.0550 time to fit residues: 7.9920 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.154508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116647 restraints weight = 12115.248| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.38 r_work: 0.3527 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.104 Angle : 0.487 9.047 11298 Z= 0.239 Chirality : 0.038 0.141 1401 Planarity : 0.003 0.035 1407 Dihedral : 4.571 58.529 1229 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.11 % Allowed : 17.32 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.26), residues: 1115 helix: 2.53 (0.19), residues: 770 sheet: -0.14 (0.68), residues: 68 loop : -0.09 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 878 TYR 0.008 0.001 TYR A 378 PHE 0.013 0.001 PHE A 738 TRP 0.005 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8262) covalent geometry : angle 0.48725 / 0.24 (11298) hydrogen bonds : bond 0.03440 / 2.35 ( 574) hydrogen bonds : angle 3.53766 / 2.56 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7136 (mpt180) REVERT: A 417 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 469 LEU cc_start: 0.8065 (tt) cc_final: 0.7804 (mp) REVERT: A 485 GLN cc_start: 0.8182 (tt0) cc_final: 0.7674 (tm-30) REVERT: A 592 LEU cc_start: 0.8410 (tp) cc_final: 0.8017 (mp) REVERT: A 721 SER cc_start: 0.8877 (t) cc_final: 0.8631 (m) REVERT: A 730 MET cc_start: 0.8368 (mmm) cc_final: 0.7826 (mtt) REVERT: A 849 ASN cc_start: 0.7476 (m-40) cc_final: 0.7075 (t0) REVERT: A 1014 SER cc_start: 0.8799 (t) cc_final: 0.8229 (p) REVERT: A 1191 GLN cc_start: 0.6871 (mt0) cc_final: 0.6646 (mp10) REVERT: A 1206 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7097 (mp0) outliers start: 23 outliers final: 19 residues processed: 101 average time/residue: 0.0759 time to fit residues: 10.9020 Evaluate side-chains 101 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 903 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.154205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.116790 restraints weight = 12165.895| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.37 r_work: 0.3534 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8262 Z= 0.105 Angle : 0.489 9.718 11298 Z= 0.240 Chirality : 0.038 0.140 1401 Planarity : 0.003 0.031 1407 Dihedral : 4.569 58.531 1229 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.38 % Allowed : 17.32 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.26), residues: 1115 helix: 2.54 (0.19), residues: 768 sheet: -0.14 (0.68), residues: 68 loop : -0.09 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1183 TYR 0.009 0.001 TYR A 845 PHE 0.013 0.001 PHE A 738 TRP 0.006 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 8262) covalent geometry : angle 0.48852 / 0.24 (11298) hydrogen bonds : bond 0.03459 / 2.36 ( 574) hydrogen bonds : angle 3.54253 / 2.56 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7175 (mpt180) REVERT: A 417 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8275 (mm) REVERT: A 469 LEU cc_start: 0.8074 (tt) cc_final: 0.7805 (mp) REVERT: A 485 GLN cc_start: 0.8209 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 592 LEU cc_start: 0.8416 (tp) cc_final: 0.8026 (mp) REVERT: A 721 SER cc_start: 0.8889 (t) cc_final: 0.8684 (m) REVERT: A 730 MET cc_start: 0.8370 (mmm) cc_final: 0.7839 (mtt) REVERT: A 849 ASN cc_start: 0.7517 (m-40) cc_final: 0.7134 (t0) REVERT: A 878 ARG cc_start: 0.8655 (mtm180) cc_final: 0.8206 (mpp80) REVERT: A 1014 SER cc_start: 0.8757 (t) cc_final: 0.8181 (p) REVERT: A 1191 GLN cc_start: 0.6862 (mt0) cc_final: 0.6642 (mp10) REVERT: A 1206 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 1320 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8478 (mptt) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.0782 time to fit residues: 11.8454 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1206 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 54 optimal weight: 0.2980 chunk 47 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 1.0664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120001 restraints weight = 12253.007| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.44 r_work: 0.3466 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8262 Z= 0.133 Angle : 0.518 9.516 11298 Z= 0.253 Chirality : 0.039 0.143 1401 Planarity : 0.003 0.033 1407 Dihedral : 4.713 59.985 1229 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.71 % Allowed : 18.00 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.26), residues: 1115 helix: 2.43 (0.19), residues: 768 sheet: -0.16 (0.67), residues: 68 loop : -0.03 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1183 TYR 0.010 0.001 TYR A 845 PHE 0.011 0.001 PHE A 738 TRP 0.006 0.001 TRP A 430 HIS 0.005 0.001 HIS A 867 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 8262) covalent geometry : angle 0.51802 / 0.25 (11298) hydrogen bonds : bond 0.03753 / 2.56 ( 574) hydrogen bonds : angle 3.62384 / 2.62 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.40 seconds wall clock time: 34 minutes 8.99 seconds (2048.99 seconds total)