Starting phenix.real_space_refine on Sat Jun 7 00:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_32535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_32535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_32535.map" model { file = "/net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_32535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wit_32535/06_2025/7wit_32535.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 21, 'HIS:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 20, 'ARG:plan': 20} 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: 5.32, per 1000 atoms: 0.66 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: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.91 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: 2.96 Time building geometry restraints manager: 2.53 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: 1.300 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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 : 4.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (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 TRP 0.011 0.001 TRP A 739 HIS 0.002 0.001 HIS A 293 PHE 0.010 0.001 PHE A1217 TYR 0.011 0.001 TYR A 230 ARG 0.002 0.000 ARG A1314 Details of bonding type rmsd hydrogen bonds : bond 0.26183 ( 574) hydrogen bonds : angle 8.33791 ( 1686) covalent geometry : bond 0.00480 ( 8262) covalent geometry : angle 0.56518 (11298) *********************** 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 : 0.858 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: 0.7621 (mp) REVERT: A 679 VAL cc_start: 0.8567 (t) cc_final: 0.8183 (p) REVERT: A 781 ASN cc_start: 0.8563 (t0) cc_final: 0.8345 (m-40) REVERT: A 903 MET cc_start: 0.7218 (mmm) cc_final: 0.6015 (mmm) REVERT: A 1018 PHE cc_start: 0.7032 (t80) cc_final: 0.6646 (t80) REVERT: A 1253 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: A 1296 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7960 (t0) outliers start: 23 outliers final: 4 residues processed: 150 average time/residue: 0.2321 time to fit residues: 46.2983 Evaluate side-chains 94 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 1253 GLU Chi-restraints excluded: chain A residue 1296 ASN 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 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.0050 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 836 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.150737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112891 restraints weight = 12212.915| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.51 r_work: 0.3454 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2260 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 : 0.542 8.262 11298 Z= 0.281 Chirality : 0.040 0.146 1401 Planarity : 0.004 0.035 1407 Dihedral : 7.375 58.659 1273 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.98 % Allowed : 11.64 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1115 helix: 1.16 (0.18), residues: 767 sheet: -0.30 (0.68), residues: 69 loop : -0.21 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 430 HIS 0.003 0.001 HIS A1098 PHE 0.027 0.001 PHE A 738 TYR 0.015 0.001 TYR A 230 ARG 0.015 0.001 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.04881 ( 574) hydrogen bonds : angle 4.39049 ( 1686) covalent geometry : bond 0.00269 ( 8262) covalent geometry : angle 0.54218 (11298) *********************** 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: 22 poor density : 100 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7052 (mpt180) REVERT: A 469 LEU cc_start: 0.7919 (tt) cc_final: 0.7563 (mp) REVERT: A 592 LEU cc_start: 0.8078 (tp) cc_final: 0.7635 (mp) REVERT: A 721 SER cc_start: 0.8978 (t) cc_final: 0.8636 (m) REVERT: A 836 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: A 903 MET cc_start: 0.7233 (mmm) cc_final: 0.6010 (mmm) REVERT: A 1191 GLN cc_start: 0.6989 (mt0) cc_final: 0.6661 (mp10) REVERT: A 1287 TYR cc_start: 0.8720 (m-80) cc_final: 0.8347 (m-80) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 0.1850 time to fit residues: 30.2481 Evaluate side-chains 90 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN 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 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 30 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 836 GLN A1296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.158013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117671 restraints weight = 12618.962| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.67 r_work: 0.3442 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8262 Z= 0.123 Angle : 0.513 6.606 11298 Z= 0.261 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.034 1407 Dihedral : 6.670 58.980 1267 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.89 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1115 helix: 1.70 (0.19), residues: 770 sheet: -0.26 (0.68), residues: 69 loop : -0.23 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 PHE 0.020 0.001 PHE A 738 TYR 0.020 0.001 TYR A 378 ARG 0.008 0.001 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 574) hydrogen bonds : angle 3.96916 ( 1686) covalent geometry : bond 0.00267 ( 8262) covalent geometry : angle 0.51320 (11298) *********************** 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: 14 poor density : 81 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7018 (mpt180) REVERT: A 469 LEU cc_start: 0.7986 (tt) cc_final: 0.7622 (mp) REVERT: A 494 GLU cc_start: 0.8139 (tp30) cc_final: 0.7907 (tp30) REVERT: A 592 LEU cc_start: 0.8184 (tp) cc_final: 0.7685 (mp) REVERT: A 721 SER cc_start: 0.8989 (t) cc_final: 0.8740 (m) REVERT: A 836 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: A 903 MET cc_start: 0.7272 (mmm) cc_final: 0.6110 (mmm) REVERT: A 1191 GLN cc_start: 0.6812 (mt0) cc_final: 0.6542 (mp10) outliers start: 14 outliers final: 8 residues processed: 91 average time/residue: 0.1739 time to fit residues: 23.1558 Evaluate side-chains 83 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4068 r_free = 0.4068 target = 0.154669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115400 restraints weight = 12497.508| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.63 r_work: 0.3422 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8262 Z= 0.148 Angle : 0.519 6.135 11298 Z= 0.262 Chirality : 0.040 0.152 1401 Planarity : 0.003 0.034 1407 Dihedral : 6.457 58.536 1264 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.38 % Allowed : 15.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.26), residues: 1115 helix: 1.89 (0.19), residues: 769 sheet: -0.18 (0.67), residues: 70 loop : -0.28 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 430 HIS 0.004 0.001 HIS A1024 PHE 0.016 0.001 PHE A 738 TYR 0.012 0.001 TYR A 845 ARG 0.005 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 574) hydrogen bonds : angle 3.89615 ( 1686) covalent geometry : bond 0.00345 ( 8262) covalent geometry : angle 0.51944 (11298) *********************** 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: 25 poor density : 84 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6965 (mpt180) REVERT: A 469 LEU cc_start: 0.7966 (tt) cc_final: 0.7568 (mp) REVERT: A 485 GLN cc_start: 0.7948 (tt0) cc_final: 0.7348 (tm-30) REVERT: A 494 GLU cc_start: 0.8121 (tp30) cc_final: 0.7889 (tp30) REVERT: A 592 LEU cc_start: 0.8161 (tp) cc_final: 0.7751 (mp) REVERT: A 721 SER cc_start: 0.8844 (t) cc_final: 0.8561 (m) REVERT: A 739 TRP cc_start: 0.4258 (OUTLIER) cc_final: 0.4013 (t60) REVERT: A 836 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 878 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.8490 (mtm110) REVERT: A 903 MET cc_start: 0.7369 (mmm) cc_final: 0.6261 (mmm) REVERT: A 1191 GLN cc_start: 0.6802 (mt0) cc_final: 0.6496 (mp10) REVERT: A 1206 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7483 (mp0) outliers start: 25 outliers final: 18 residues processed: 105 average time/residue: 0.1705 time to fit residues: 26.3816 Evaluate side-chains 95 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 461 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 10 optimal weight: 0.0270 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.155749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116625 restraints weight = 12376.584| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.63 r_work: 0.3455 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8262 Z= 0.131 Angle : 0.508 6.627 11298 Z= 0.253 Chirality : 0.039 0.139 1401 Planarity : 0.003 0.033 1407 Dihedral : 6.346 58.977 1264 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.06 % Allowed : 15.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1115 helix: 2.03 (0.19), residues: 769 sheet: -0.18 (0.66), residues: 70 loop : -0.29 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 PHE 0.015 0.001 PHE A 738 TYR 0.014 0.001 TYR A 845 ARG 0.003 0.000 ARG A1111 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 574) hydrogen bonds : angle 3.79441 ( 1686) covalent geometry : bond 0.00301 ( 8262) covalent geometry : angle 0.50758 (11298) *********************** 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: 30 poor density : 79 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 297 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7002 (mpt180) REVERT: A 469 LEU cc_start: 0.7936 (tt) cc_final: 0.7560 (mp) REVERT: A 485 GLN cc_start: 0.7991 (tt0) cc_final: 0.7327 (tm-30) REVERT: A 592 LEU cc_start: 0.8188 (tp) cc_final: 0.7766 (mp) REVERT: A 721 SER cc_start: 0.8848 (t) cc_final: 0.8595 (m) REVERT: A 739 TRP cc_start: 0.4283 (OUTLIER) cc_final: 0.4028 (t60) REVERT: A 878 ARG cc_start: 0.8674 (tmm-80) cc_final: 0.8451 (mtm110) REVERT: A 903 MET cc_start: 0.7455 (mmm) cc_final: 0.6347 (mmm) REVERT: A 1014 SER cc_start: 0.8711 (t) cc_final: 0.8027 (p) REVERT: A 1191 GLN cc_start: 0.6696 (mt0) cc_final: 0.6418 (mp10) REVERT: A 1206 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7468 (mp0) outliers start: 30 outliers final: 21 residues processed: 103 average time/residue: 0.1748 time to fit residues: 26.4188 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 499 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 1066 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1079 CYS 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 1431 LEU Chi-restraints excluded: chain A residue 1435 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117903 restraints weight = 12197.814| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.51 r_work: 0.3455 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8262 Z= 0.117 Angle : 0.484 6.703 11298 Z= 0.242 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.032 1407 Dihedral : 6.176 59.806 1264 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.84 % Allowed : 16.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1115 helix: 2.20 (0.19), residues: 769 sheet: -0.19 (0.66), residues: 70 loop : -0.27 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 430 HIS 0.003 0.001 HIS A1024 PHE 0.014 0.001 PHE A 738 TYR 0.018 0.001 TYR A 845 ARG 0.003 0.000 ARG A 370 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 574) hydrogen bonds : angle 3.70402 ( 1686) covalent geometry : bond 0.00264 ( 8262) covalent geometry : angle 0.48385 (11298) *********************** 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 107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7963 (ttm170) cc_final: 0.7637 (ttt90) REVERT: A 469 LEU cc_start: 0.8140 (tt) cc_final: 0.7786 (mp) REVERT: A 485 GLN cc_start: 0.8018 (tt0) cc_final: 0.7394 (tm-30) REVERT: A 592 LEU cc_start: 0.8271 (tp) cc_final: 0.7848 (mp) REVERT: A 721 SER cc_start: 0.8883 (t) cc_final: 0.8669 (m) REVERT: A 739 TRP cc_start: 0.4231 (OUTLIER) cc_final: 0.3952 (t60) REVERT: A 903 MET cc_start: 0.7452 (mmm) cc_final: 0.6456 (mmm) REVERT: A 1014 SER cc_start: 0.8732 (t) cc_final: 0.8087 (p) REVERT: A 1191 GLN cc_start: 0.6700 (mt0) cc_final: 0.6436 (mp10) outliers start: 21 outliers final: 18 residues processed: 104 average time/residue: 0.1705 time to fit residues: 25.9368 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain A residue 499 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 1073 SER Chi-restraints excluded: chain A residue 1079 CYS 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 1369 ILE Chi-restraints excluded: chain A residue 1423 SER Chi-restraints excluded: chain A residue 1431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117833 restraints weight = 12270.879| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.59 r_work: 0.3457 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8262 Z= 0.110 Angle : 0.481 7.021 11298 Z= 0.241 Chirality : 0.038 0.140 1401 Planarity : 0.003 0.049 1407 Dihedral : 5.842 60.293 1260 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.38 % Allowed : 17.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.26), residues: 1115 helix: 2.30 (0.19), residues: 769 sheet: -0.22 (0.66), residues: 70 loop : -0.28 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1247 HIS 0.003 0.001 HIS A1024 PHE 0.015 0.001 PHE A 738 TYR 0.019 0.001 TYR A 845 ARG 0.011 0.000 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 574) hydrogen bonds : angle 3.66603 ( 1686) covalent geometry : bond 0.00245 ( 8262) covalent geometry : angle 0.48136 (11298) *********************** 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 108 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7559 (ttt90) REVERT: A 297 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6963 (mpt180) REVERT: A 469 LEU cc_start: 0.8080 (tt) cc_final: 0.7738 (mp) REVERT: A 485 GLN cc_start: 0.7978 (tt0) cc_final: 0.7305 (tm-30) REVERT: A 592 LEU cc_start: 0.8195 (tp) cc_final: 0.7774 (mp) REVERT: A 721 SER cc_start: 0.8823 (t) cc_final: 0.8615 (m) REVERT: A 739 TRP cc_start: 0.4179 (OUTLIER) cc_final: 0.3866 (t60) REVERT: A 903 MET cc_start: 0.7466 (mmm) cc_final: 0.6492 (mmm) REVERT: A 1014 SER cc_start: 0.8693 (t) cc_final: 0.8031 (p) REVERT: A 1038 THR cc_start: 0.8441 (p) cc_final: 0.8211 (p) REVERT: A 1191 GLN cc_start: 0.6536 (mt0) cc_final: 0.6270 (mp10) REVERT: A 1206 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7440 (mp0) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 0.1923 time to fit residues: 28.6882 Evaluate side-chains 99 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 461 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.151923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114847 restraints weight = 12522.264| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.49 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: 0.7718 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8262 Z= 0.222 Angle : 0.594 7.453 11298 Z= 0.295 Chirality : 0.042 0.143 1401 Planarity : 0.004 0.044 1407 Dihedral : 6.124 59.491 1260 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.25 % Allowed : 17.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.26), residues: 1115 helix: 1.92 (0.19), residues: 768 sheet: -0.15 (0.66), residues: 68 loop : -0.36 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 778 HIS 0.005 0.001 HIS A1024 PHE 0.013 0.001 PHE A1223 TYR 0.017 0.001 TYR A 845 ARG 0.008 0.001 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 574) hydrogen bonds : angle 3.94560 ( 1686) covalent geometry : bond 0.00532 ( 8262) covalent geometry : angle 0.59405 (11298) *********************** 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 107 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7689 (m-80) cc_final: 0.6611 (m-80) REVERT: A 265 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7724 (ttt90) REVERT: A 297 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7030 (mpt180) REVERT: A 469 LEU cc_start: 0.8074 (tt) cc_final: 0.7591 (mp) REVERT: A 485 GLN cc_start: 0.8036 (tt0) cc_final: 0.7577 (tm-30) REVERT: A 592 LEU cc_start: 0.8380 (tp) cc_final: 0.7940 (mp) REVERT: A 849 ASN cc_start: 0.7547 (m-40) cc_final: 0.7190 (t0) REVERT: A 903 MET cc_start: 0.7687 (mmm) cc_final: 0.6407 (mmm) REVERT: A 1014 SER cc_start: 0.8763 (t) cc_final: 0.8094 (p) REVERT: A 1191 GLN cc_start: 0.6820 (mt0) cc_final: 0.6505 (mp10) REVERT: A 1206 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7529 (mp0) outliers start: 24 outliers final: 21 residues processed: 100 average time/residue: 0.1920 time to fit residues: 27.5520 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 701 ILE Chi-restraints excluded: chain A residue 737 VAL 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 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 76 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.156829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119756 restraints weight = 12389.756| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.54 r_work: 0.3463 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8262 Z= 0.111 Angle : 0.491 7.630 11298 Z= 0.246 Chirality : 0.039 0.140 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.874 58.888 1260 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.17 % Allowed : 18.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1115 helix: 2.34 (0.19), residues: 758 sheet: -0.35 (0.65), residues: 70 loop : -0.30 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 430 HIS 0.003 0.001 HIS A1098 PHE 0.015 0.001 PHE A 738 TYR 0.023 0.001 TYR A 845 ARG 0.003 0.000 ARG A 835 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 574) hydrogen bonds : angle 3.72072 ( 1686) covalent geometry : bond 0.00243 ( 8262) covalent geometry : angle 0.49138 (11298) *********************** 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 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7623 (ttt90) REVERT: A 469 LEU cc_start: 0.8131 (tt) cc_final: 0.7711 (mp) REVERT: A 485 GLN cc_start: 0.7991 (tt0) cc_final: 0.7412 (tm-30) REVERT: A 592 LEU cc_start: 0.8308 (tp) cc_final: 0.7881 (mp) REVERT: A 849 ASN cc_start: 0.7508 (m-40) cc_final: 0.7114 (t0) REVERT: A 903 MET cc_start: 0.7536 (mmm) cc_final: 0.6624 (mmm) REVERT: A 1014 SER cc_start: 0.8732 (t) cc_final: 0.8093 (p) REVERT: A 1038 THR cc_start: 0.8386 (p) cc_final: 0.8175 (p) REVERT: A 1191 GLN cc_start: 0.6612 (mt0) cc_final: 0.6340 (mp10) REVERT: A 1206 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7486 (mp0) outliers start: 16 outliers final: 13 residues processed: 98 average time/residue: 0.2462 time to fit residues: 34.5207 Evaluate side-chains 96 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE 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 1106 ILE 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 Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.153135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116482 restraints weight = 12321.431| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.47 r_work: 0.3421 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8262 Z= 0.199 Angle : 0.573 8.395 11298 Z= 0.285 Chirality : 0.042 0.187 1401 Planarity : 0.003 0.042 1407 Dihedral : 6.011 59.996 1260 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.57 % Allowed : 18.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1115 helix: 2.06 (0.19), residues: 761 sheet: -0.21 (0.65), residues: 68 loop : -0.38 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 430 HIS 0.005 0.001 HIS A1024 PHE 0.013 0.001 PHE A 738 TYR 0.020 0.001 TYR A 845 ARG 0.009 0.001 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 574) hydrogen bonds : angle 3.87591 ( 1686) covalent geometry : bond 0.00477 ( 8262) covalent geometry : angle 0.57341 (11298) ********************** 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 106 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7716 (ttt90) REVERT: A 297 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7042 (mpt180) REVERT: A 469 LEU cc_start: 0.8071 (tt) cc_final: 0.7623 (mp) REVERT: A 485 GLN cc_start: 0.8044 (tt0) cc_final: 0.7509 (tm-30) REVERT: A 592 LEU cc_start: 0.8358 (tp) cc_final: 0.7920 (mp) REVERT: A 849 ASN cc_start: 0.7457 (m-40) cc_final: 0.7146 (t0) REVERT: A 903 MET cc_start: 0.7667 (mmm) cc_final: 0.6394 (mmm) REVERT: A 1014 SER cc_start: 0.8764 (t) cc_final: 0.8112 (p) REVERT: A 1191 GLN cc_start: 0.6738 (mt0) cc_final: 0.6444 (mp10) REVERT: A 1206 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7542 (mp0) REVERT: A 1461 LYS cc_start: 0.7851 (tptt) cc_final: 0.7576 (tptp) outliers start: 19 outliers final: 18 residues processed: 101 average time/residue: 0.3375 time to fit residues: 48.5365 Evaluate side-chains 102 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 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 1066 MET Chi-restraints excluded: chain A residue 1073 SER Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1291 VAL 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 Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118479 restraints weight = 12327.090| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.46 r_work: 0.3463 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3749 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= 0.115 Angle : 0.504 7.710 11298 Z= 0.251 Chirality : 0.039 0.191 1401 Planarity : 0.003 0.032 1407 Dihedral : 5.803 58.730 1260 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.89 % Allowed : 19.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.26), residues: 1115 helix: 2.27 (0.19), residues: 763 sheet: -0.36 (0.64), residues: 70 loop : -0.25 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 430 HIS 0.003 0.001 HIS A1098 PHE 0.015 0.001 PHE A 738 TYR 0.023 0.001 TYR A 845 ARG 0.003 0.000 ARG A 878 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 574) hydrogen bonds : angle 3.74895 ( 1686) covalent geometry : bond 0.00254 ( 8262) covalent geometry : angle 0.50405 (11298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.52 seconds wall clock time: 67 minutes 36.58 seconds (4056.58 seconds total)