Starting phenix.real_space_refine on Tue Mar 3 19:23:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wit_32535/03_2026/7wit_32535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wit_32535/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wit_32535/03_2026/7wit_32535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wit_32535/03_2026/7wit_32535.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wit_32535/03_2026/7wit_32535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wit_32535/03_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-5986/lib/python3.9/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: 1.77, per 1000 atoms: 0.22 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: 0.69 Conformation dependent library (CDL) restraints added in 360.6 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: 0.26 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: 1.30 Time building geometry restraints manager: 0.86 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 - 12.66: 4412 12.66 - 25.31: 349 25.31 - 37.97: 94 37.97 - 50.62: 32 50.62 - 63.28: 13 Dihedral angle restraints: 4900 sinusoidal: 1602 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 4897 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.480 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 11.490 63.276 2754 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 covalent geometry : bond 0.00480 ( 8262) covalent geometry : angle 0.56518 (11298) hydrogen bonds : bond 0.26183 ( 574) hydrogen bonds : angle 8.33791 ( 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 : 0.291 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: 0.1022 time to fit residues: 20.3394 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 : 0.307 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4038 r_free = 0.4038 target = 0.152081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.112708 restraints weight = 12664.338| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.62 r_work: 0.3432 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8262 Z= 0.135 Angle : 0.542 8.076 11298 Z= 0.282 Chirality : 0.040 0.143 1401 Planarity : 0.004 0.035 1407 Dihedral : 7.157 58.755 1268 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.84 % Allowed : 11.91 % 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: 0.99 (0.25), residues: 1115 helix: 1.14 (0.18), residues: 767 sheet: -0.31 (0.68), residues: 69 loop : -0.21 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 878 TYR 0.014 0.001 TYR A 230 PHE 0.029 0.001 PHE A 738 TRP 0.010 0.001 TRP A 430 HIS 0.003 0.001 HIS A1098 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8262) covalent geometry : angle 0.54236 (11298) hydrogen bonds : bond 0.04854 ( 574) hydrogen bonds : angle 4.36769 ( 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 122 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7063 (mpt180) REVERT: A 469 LEU cc_start: 0.7914 (tt) cc_final: 0.7564 (mp) REVERT: A 592 LEU cc_start: 0.8075 (tp) cc_final: 0.7633 (mp) REVERT: A 721 SER cc_start: 0.8964 (t) cc_final: 0.8573 (m) REVERT: A 836 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 878 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8361 (ttp80) REVERT: A 903 MET cc_start: 0.7234 (mmm) cc_final: 0.6020 (mmm) REVERT: A 1191 GLN cc_start: 0.6976 (mt0) cc_final: 0.6663 (mp10) REVERT: A 1287 TYR cc_start: 0.8709 (m-80) cc_final: 0.8327 (m-80) REVERT: A 1290 MET cc_start: 0.8243 (tpp) cc_final: 0.7978 (mmt) outliers start: 21 outliers final: 9 residues processed: 117 average time/residue: 0.0837 time to fit residues: 13.6723 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 304 THR 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 1350 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4015 r_free = 0.4015 target = 0.148535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109604 restraints weight = 12534.750| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.59 r_work: 0.3416 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8262 Z= 0.161 Angle : 0.546 6.525 11298 Z= 0.276 Chirality : 0.040 0.143 1401 Planarity : 0.003 0.035 1407 Dihedral : 6.782 59.550 1267 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.71 % Allowed : 14.07 % Favored : 83.22 % 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: 1.46 (0.26), residues: 1115 helix: 1.58 (0.19), residues: 767 sheet: -0.37 (0.67), residues: 69 loop : -0.26 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 835 TYR 0.012 0.001 TYR A 230 PHE 0.018 0.001 PHE A 738 TRP 0.009 0.001 TRP A 430 HIS 0.004 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8262) covalent geometry : angle 0.54630 (11298) hydrogen bonds : bond 0.04591 ( 574) hydrogen bonds : angle 4.07667 ( 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 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7039 (mpt180) REVERT: A 469 LEU cc_start: 0.7946 (tt) cc_final: 0.7524 (mp) REVERT: A 494 GLU cc_start: 0.8074 (tp30) cc_final: 0.7833 (tp30) REVERT: A 592 LEU cc_start: 0.8162 (tp) cc_final: 0.7640 (mp) REVERT: A 721 SER cc_start: 0.8960 (t) cc_final: 0.8692 (m) REVERT: A 836 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 903 MET cc_start: 0.7317 (mmm) cc_final: 0.6097 (mmm) REVERT: A 1191 GLN cc_start: 0.6854 (mt0) cc_final: 0.6572 (mp10) outliers start: 20 outliers final: 15 residues processed: 96 average time/residue: 0.0735 time to fit residues: 10.3670 Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 461 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 588 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 1079 CYS 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 1423 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.111085 restraints weight = 12531.920| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.56 r_work: 0.3431 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2940 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= 0.124 Angle : 0.501 6.110 11298 Z= 0.253 Chirality : 0.040 0.159 1401 Planarity : 0.003 0.033 1407 Dihedral : 6.586 58.598 1266 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 16.10 % Favored : 81.33 % 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: 1.79 (0.26), residues: 1115 helix: 1.89 (0.19), residues: 769 sheet: -0.31 (0.65), residues: 70 loop : -0.31 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 878 TYR 0.013 0.001 TYR A 845 PHE 0.017 0.001 PHE A 738 TRP 0.008 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8262) covalent geometry : angle 0.50062 (11298) hydrogen bonds : bond 0.04078 ( 574) hydrogen bonds : angle 3.87703 ( 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 106 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7032 (mpt180) REVERT: A 469 LEU cc_start: 0.7964 (tt) cc_final: 0.7595 (mp) REVERT: A 485 GLN cc_start: 0.7993 (tt0) cc_final: 0.7418 (tm-30) REVERT: A 494 GLU cc_start: 0.8176 (tp30) cc_final: 0.7951 (tp30) REVERT: A 592 LEU cc_start: 0.8177 (tp) cc_final: 0.7779 (mp) REVERT: A 721 SER cc_start: 0.9023 (t) cc_final: 0.8774 (m) REVERT: A 739 TRP cc_start: 0.4272 (OUTLIER) cc_final: 0.4020 (t60) REVERT: A 836 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: A 903 MET cc_start: 0.7390 (mmm) cc_final: 0.6263 (mmm) REVERT: A 1014 SER cc_start: 0.8747 (t) cc_final: 0.8076 (p) REVERT: A 1191 GLN cc_start: 0.6892 (mt0) cc_final: 0.6598 (mp10) REVERT: A 1206 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7527 (mp0) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.0734 time to fit residues: 10.8259 Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP Chi-restraints excluded: chain A residue 836 GLN Chi-restraints excluded: chain A residue 1066 MET 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 1435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.157013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117713 restraints weight = 12533.543| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.67 r_work: 0.3468 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8262 Z= 0.113 Angle : 0.492 7.103 11298 Z= 0.245 Chirality : 0.039 0.139 1401 Planarity : 0.003 0.042 1407 Dihedral : 6.332 59.940 1264 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.52 % Allowed : 16.64 % Favored : 79.84 % 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: 2.04 (0.26), residues: 1115 helix: 2.09 (0.19), residues: 769 sheet: -0.17 (0.66), residues: 70 loop : -0.31 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 878 TYR 0.015 0.001 TYR A 845 PHE 0.016 0.001 PHE A 738 TRP 0.007 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8262) covalent geometry : angle 0.49158 (11298) hydrogen bonds : bond 0.03856 ( 574) hydrogen bonds : angle 3.74323 ( 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 109 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.6983 (mpt180) REVERT: A 469 LEU cc_start: 0.8090 (tt) cc_final: 0.7781 (mp) REVERT: A 485 GLN cc_start: 0.7961 (tt0) cc_final: 0.7301 (tm-30) REVERT: A 592 LEU cc_start: 0.8186 (tp) cc_final: 0.7776 (mp) REVERT: A 721 SER cc_start: 0.8840 (t) cc_final: 0.8583 (m) REVERT: A 739 TRP cc_start: 0.4214 (OUTLIER) cc_final: 0.3938 (t60) REVERT: A 903 MET cc_start: 0.7370 (mmm) cc_final: 0.6253 (mmm) REVERT: A 1014 SER cc_start: 0.8704 (t) cc_final: 0.8035 (p) REVERT: A 1191 GLN cc_start: 0.6680 (mt0) cc_final: 0.6422 (mp10) REVERT: A 1206 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7472 (mp0) outliers start: 26 outliers final: 18 residues processed: 104 average time/residue: 0.0682 time to fit residues: 10.5712 Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 429 MET 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 607 VAL Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP 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 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.157408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.118659 restraints weight = 12361.250| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.62 r_work: 0.3470 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8262 Z= 0.104 Angle : 0.473 6.973 11298 Z= 0.237 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.034 1407 Dihedral : 6.090 59.905 1264 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.84 % Allowed : 16.78 % Favored : 80.38 % 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: 2.28 (0.26), residues: 1115 helix: 2.32 (0.19), residues: 766 sheet: -0.16 (0.66), residues: 70 loop : -0.34 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 878 TYR 0.019 0.001 TYR A 845 PHE 0.014 0.001 PHE A 738 TRP 0.008 0.001 TRP A 430 HIS 0.002 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8262) covalent geometry : angle 0.47296 (11298) hydrogen bonds : bond 0.03670 ( 574) hydrogen bonds : angle 3.65064 ( 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 108 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 469 LEU cc_start: 0.8040 (tt) cc_final: 0.7736 (mp) REVERT: A 485 GLN cc_start: 0.7974 (tt0) cc_final: 0.7309 (tm-30) REVERT: A 592 LEU cc_start: 0.8366 (tp) cc_final: 0.7956 (mp) REVERT: A 721 SER cc_start: 0.8832 (t) cc_final: 0.8615 (m) REVERT: A 739 TRP cc_start: 0.4125 (OUTLIER) cc_final: 0.3813 (t60) REVERT: A 903 MET cc_start: 0.7371 (mmm) cc_final: 0.6381 (mmm) REVERT: A 1014 SER cc_start: 0.8706 (t) cc_final: 0.8050 (p) REVERT: A 1191 GLN cc_start: 0.6610 (mt0) cc_final: 0.6360 (mp10) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.0654 time to fit residues: 10.0076 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 461 LEU 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 739 TRP 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 Chi-restraints excluded: chain A residue 1435 THR Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 51 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.153843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.115731 restraints weight = 12268.163| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.41 r_work: 0.3497 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8262 Z= 0.103 Angle : 0.479 9.572 11298 Z= 0.237 Chirality : 0.038 0.141 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.754 61.138 1260 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 17.46 % Favored : 79.97 % 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: 2.37 (0.26), residues: 1115 helix: 2.40 (0.19), residues: 765 sheet: -0.16 (0.66), residues: 70 loop : -0.31 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 878 TYR 0.019 0.001 TYR A 845 PHE 0.015 0.001 PHE A 738 TRP 0.006 0.001 TRP A1247 HIS 0.002 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8262) covalent geometry : angle 0.47937 (11298) hydrogen bonds : bond 0.03561 ( 574) hydrogen bonds : angle 3.61367 ( 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 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 469 LEU cc_start: 0.8088 (tt) cc_final: 0.7843 (mp) REVERT: A 485 GLN cc_start: 0.8002 (tt0) cc_final: 0.7494 (tm-30) REVERT: A 592 LEU cc_start: 0.8499 (tp) cc_final: 0.8107 (mp) REVERT: A 721 SER cc_start: 0.8854 (t) cc_final: 0.8638 (m) REVERT: A 730 MET cc_start: 0.8359 (mmm) cc_final: 0.7797 (mtt) REVERT: A 739 TRP cc_start: 0.4197 (OUTLIER) cc_final: 0.3892 (t60) REVERT: A 849 ASN cc_start: 0.7448 (m-40) cc_final: 0.7077 (t0) REVERT: A 903 MET cc_start: 0.7454 (mmm) cc_final: 0.6594 (mmm) REVERT: A 1014 SER cc_start: 0.8770 (t) cc_final: 0.8167 (p) REVERT: A 1206 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7550 (mp0) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.0786 time to fit residues: 11.3204 Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 739 TRP 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 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.157167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120106 restraints weight = 12211.423| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.49 r_work: 0.3489 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3593 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= 0.114 Angle : 0.493 9.481 11298 Z= 0.243 Chirality : 0.039 0.179 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.698 62.753 1260 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.30 % Allowed : 18.67 % Favored : 79.03 % 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: 2.38 (0.26), residues: 1115 helix: 2.40 (0.19), residues: 765 sheet: -0.17 (0.66), residues: 70 loop : -0.25 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 878 TYR 0.021 0.001 TYR A 845 PHE 0.014 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 covalent geometry : bond 0.00256 ( 8262) covalent geometry : angle 0.49346 (11298) hydrogen bonds : bond 0.03667 ( 574) hydrogen bonds : angle 3.64535 ( 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 100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 469 LEU cc_start: 0.8015 (tt) cc_final: 0.7741 (mp) REVERT: A 485 GLN cc_start: 0.7999 (tt0) cc_final: 0.7454 (tm-30) REVERT: A 592 LEU cc_start: 0.8342 (tp) cc_final: 0.7924 (mp) REVERT: A 721 SER cc_start: 0.8843 (t) cc_final: 0.8614 (m) REVERT: A 730 MET cc_start: 0.8348 (mmm) cc_final: 0.7868 (mtt) REVERT: A 739 TRP cc_start: 0.4253 (OUTLIER) cc_final: 0.3980 (t60) REVERT: A 849 ASN cc_start: 0.7512 (m-40) cc_final: 0.7075 (t0) REVERT: A 903 MET cc_start: 0.7529 (mmm) cc_final: 0.6659 (mmm) REVERT: A 1014 SER cc_start: 0.8744 (t) cc_final: 0.8117 (p) REVERT: A 1206 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7526 (mp0) outliers start: 17 outliers final: 16 residues processed: 96 average time/residue: 0.0674 time to fit residues: 9.7543 Evaluate side-chains 97 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 304 THR 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 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP 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 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: 8.9990 chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.152856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.114920 restraints weight = 12181.025| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.38 r_work: 0.3488 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8262 Z= 0.115 Angle : 0.494 9.131 11298 Z= 0.244 Chirality : 0.039 0.155 1401 Planarity : 0.003 0.031 1407 Dihedral : 5.621 63.491 1260 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.57 % Allowed : 18.54 % Favored : 78.89 % 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: 2.39 (0.26), residues: 1115 helix: 2.40 (0.19), residues: 766 sheet: -0.19 (0.66), residues: 70 loop : -0.25 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1215 TYR 0.021 0.001 TYR A 845 PHE 0.014 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 covalent geometry : bond 0.00262 ( 8262) covalent geometry : angle 0.49394 (11298) hydrogen bonds : bond 0.03653 ( 574) hydrogen bonds : angle 3.63400 ( 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 103 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7691 (ttt90) REVERT: A 297 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7165 (mpt180) REVERT: A 469 LEU cc_start: 0.8088 (tt) cc_final: 0.7801 (mp) REVERT: A 485 GLN cc_start: 0.8194 (tt0) cc_final: 0.7649 (tm-30) REVERT: A 592 LEU cc_start: 0.8400 (tp) cc_final: 0.7985 (mp) REVERT: A 730 MET cc_start: 0.8404 (mmm) cc_final: 0.7889 (mtt) REVERT: A 739 TRP cc_start: 0.4393 (OUTLIER) cc_final: 0.4124 (t60) REVERT: A 849 ASN cc_start: 0.7593 (m-40) cc_final: 0.7166 (t0) REVERT: A 903 MET cc_start: 0.7552 (mmm) cc_final: 0.6695 (mmm) REVERT: A 1014 SER cc_start: 0.8824 (t) cc_final: 0.8229 (p) REVERT: A 1206 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7693 (mp0) REVERT: A 1461 LYS cc_start: 0.8145 (tptt) cc_final: 0.7890 (tttp) outliers start: 19 outliers final: 17 residues processed: 99 average time/residue: 0.0807 time to fit residues: 11.3974 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 : 0.293 ------------------------------------------------------------------------------- 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 304 THR 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 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP 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 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: 3.9990 chunk 77 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.157599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120959 restraints weight = 12188.550| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.48 r_work: 0.3484 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8262 Z= 0.112 Angle : 0.495 8.979 11298 Z= 0.244 Chirality : 0.039 0.149 1401 Planarity : 0.003 0.031 1407 Dihedral : 5.550 64.480 1260 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.17 % Allowed : 19.08 % Favored : 78.76 % 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: 2.44 (0.26), residues: 1115 helix: 2.44 (0.19), residues: 765 sheet: -0.20 (0.66), residues: 70 loop : -0.22 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1215 TYR 0.023 0.001 TYR A 845 PHE 0.014 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 covalent geometry : bond 0.00251 ( 8262) covalent geometry : angle 0.49453 (11298) hydrogen bonds : bond 0.03602 ( 574) hydrogen bonds : angle 3.61516 ( 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 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7612 (ttt90) REVERT: A 297 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7047 (mpt180) REVERT: A 469 LEU cc_start: 0.8025 (tt) cc_final: 0.7731 (mp) REVERT: A 485 GLN cc_start: 0.8007 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 592 LEU cc_start: 0.8240 (tp) cc_final: 0.7819 (mp) REVERT: A 739 TRP cc_start: 0.4270 (OUTLIER) cc_final: 0.3981 (t60) REVERT: A 849 ASN cc_start: 0.7521 (m-40) cc_final: 0.7081 (t0) REVERT: A 903 MET cc_start: 0.7552 (mmm) cc_final: 0.6683 (mmm) REVERT: A 1014 SER cc_start: 0.8704 (t) cc_final: 0.8072 (p) REVERT: A 1461 LYS cc_start: 0.8168 (tptt) cc_final: 0.7898 (tttp) outliers start: 16 outliers final: 14 residues processed: 95 average time/residue: 0.0856 time to fit residues: 11.4750 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 TRP 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 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 106 optimal weight: 30.0000 chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.152412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.115495 restraints weight = 12465.759| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.47 r_work: 0.3396 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8262 Z= 0.236 Angle : 0.608 10.022 11298 Z= 0.302 Chirality : 0.043 0.180 1401 Planarity : 0.003 0.037 1407 Dihedral : 5.869 63.288 1260 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 18.40 % Favored : 79.03 % 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: 1.90 (0.26), residues: 1115 helix: 1.98 (0.19), residues: 765 sheet: -0.35 (0.65), residues: 70 loop : -0.24 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 878 TYR 0.018 0.002 TYR A 845 PHE 0.012 0.001 PHE A 738 TRP 0.009 0.001 TRP A 778 HIS 0.006 0.001 HIS A1024 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8262) covalent geometry : angle 0.60786 (11298) hydrogen bonds : bond 0.04442 ( 574) hydrogen bonds : angle 3.92218 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.63 seconds wall clock time: 29 minutes 11.72 seconds (1751.72 seconds total)