Starting phenix.real_space_refine on Wed Mar 4 02:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530.map" model { file = "/net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pza_20530/03_2026/6pza_20530_neut.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 34 5.16 5 Cl 1 4.86 5 C 6209 2.51 5 N 1717 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9659 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 9501 Classifications: {'peptide': 1422} Incomplete info: {'truncation_to_alanine': 543} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 1372} Chain breaks: 4 Unresolved non-hydrogen bonds: 1768 Unresolved non-hydrogen angles: 2233 Unresolved non-hydrogen dihedrals: 1378 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLU:plan': 44, 'ASP:plan': 41, 'ASN:plan1': 21, 'HIS:plan': 7, 'ARG:plan': 33, 'GLN:plan1': 32, 'PHE:plan': 17, 'TYR:plan': 2, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 833 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 94 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 17} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.77, per 1000 atoms: 0.29 Number of scatterers: 9659 At special positions: 0 Unit cell: (96.615, 110.295, 140.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 P 3 15.00 O 1695 8.00 N 1717 7.00 C 6209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 26 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 473.0 milliseconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 66.3% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 12 through 16 removed outlier: 3.613A pdb=" N ARG C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 55 removed outlier: 3.885A pdb=" N VAL C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Proline residue: C 35 - end of helix Proline residue: C 45 - end of helix Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.604A pdb=" N HIS C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS C 62 " --> pdb=" O HIS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 97 Processing helix chain 'C' and resid 108 through 130 removed outlier: 3.599A pdb=" N TYR C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 166 through 194 removed outlier: 3.993A pdb=" N CYS C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 232 through 238 removed outlier: 4.019A pdb=" N PHE C 236 " --> pdb=" O TRP C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 258 through 277 Processing helix chain 'C' and resid 283 through 314 removed outlier: 5.732A pdb=" N ARG C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 329 through 332 removed outlier: 3.897A pdb=" N HIS C 332 " --> pdb=" O LYS C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 332' Processing helix chain 'C' and resid 347 through 352 Processing helix chain 'C' and resid 355 through 398 removed outlier: 3.505A pdb=" N LEU C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLN C 374 " --> pdb=" O ARG C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 432 removed outlier: 3.510A pdb=" N ILE C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 456 Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.662A pdb=" N LEU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 504 removed outlier: 3.539A pdb=" N GLN C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.703A pdb=" N TYR C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 564 removed outlier: 4.277A pdb=" N THR C 525 " --> pdb=" O ARG C 521 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 543 " --> pdb=" O TYR C 539 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 544 " --> pdb=" O THR C 540 " (cutoff:3.500A) Proline residue: C 551 - end of helix Processing helix chain 'C' and resid 572 through 615 Proline residue: C 589 - end of helix removed outlier: 3.972A pdb=" N LEU C 592 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 594 " --> pdb=" O LEU C 590 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 595 " --> pdb=" O PHE C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 727 Processing helix chain 'C' and resid 785 through 790 Processing helix chain 'C' and resid 795 through 806 Processing helix chain 'C' and resid 808 through 815 removed outlier: 3.870A pdb=" N LEU C 815 " --> pdb=" O ASP C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 846 removed outlier: 3.698A pdb=" N GLN C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 879 Processing helix chain 'C' and resid 996 through 1009 removed outlier: 3.602A pdb=" N GLY C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1043 removed outlier: 4.494A pdb=" N LEU C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1061 through 1107 removed outlier: 3.906A pdb=" N LEU C1074 " --> pdb=" O LEU C1070 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1116 removed outlier: 4.033A pdb=" N PHE C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1135 removed outlier: 3.716A pdb=" N ILE C1121 " --> pdb=" O PRO C1117 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C1128 " --> pdb=" O ARG C1124 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1161 removed outlier: 4.000A pdb=" N LEU C1148 " --> pdb=" O SER C1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1210 removed outlier: 3.744A pdb=" N ALA C1167 " --> pdb=" O VAL C1163 " (cutoff:3.500A) Proline residue: C1170 - end of helix removed outlier: 3.720A pdb=" N ASP C1188 " --> pdb=" O VAL C1184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) Proline residue: C1199 - end of helix removed outlier: 3.587A pdb=" N VAL C1208 " --> pdb=" O PHE C1204 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C1210 " --> pdb=" O GLU C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1210 through 1218 removed outlier: 3.769A pdb=" N ILE C1214 " --> pdb=" O GLY C1210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG C1218 " --> pdb=" O ILE C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1273 removed outlier: 3.927A pdb=" N PHE C1223 " --> pdb=" O TYR C1219 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1237 " --> pdb=" O SER C1233 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS C1273 " --> pdb=" O SER C1269 " (cutoff:3.500A) Processing helix chain 'C' and resid 1278 through 1292 removed outlier: 3.522A pdb=" N GLY C1282 " --> pdb=" O ALA C1278 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1294 through 1320 removed outlier: 3.806A pdb=" N ALA C1311 " --> pdb=" O ILE C1307 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL C1312 " --> pdb=" O GLN C1308 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE C1315 " --> pdb=" O ALA C1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 1385 through 1392 Processing helix chain 'C' and resid 1414 through 1419 Processing helix chain 'C' and resid 1435 through 1441 Processing helix chain 'C' and resid 1447 through 1458 removed outlier: 3.596A pdb=" N LEU C1451 " --> pdb=" O SER C1447 " (cutoff:3.500A) Processing helix chain 'C' and resid 1460 through 1465 Processing helix chain 'C' and resid 1484 through 1498 removed outlier: 4.140A pdb=" N GLN C1488 " --> pdb=" O GLN C1484 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1531 Processing helix chain 'C' and resid 1539 through 1543 removed outlier: 3.525A pdb=" N ILE C1543 " --> pdb=" O VAL C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1564 through 1570 removed outlier: 4.193A pdb=" N SER C1568 " --> pdb=" O GLU C1564 " (cutoff:3.500A) Processing helix chain 'C' and resid 1571 through 1578 Processing sheet with id=AA1, first strand: chain 'C' and resid 338 through 340 removed outlier: 4.227A pdb=" N THR C 338 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AA3, first strand: chain 'C' and resid 852 through 853 removed outlier: 4.264A pdb=" N ILE C 901 " --> pdb=" O MET C 710 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 712 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA C 902 " --> pdb=" O GLN C 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1366 through 1368 removed outlier: 4.391A pdb=" N GLN C1346 " --> pdb=" O ILE C1404 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C1404 " --> pdb=" O GLN C1346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1352 through 1353 Processing sheet with id=AA6, first strand: chain 'C' and resid 1375 through 1376 Processing sheet with id=AA7, first strand: chain 'C' and resid 1422 through 1424 removed outlier: 6.898A pdb=" N SER C1423 " --> pdb=" O ILE C1504 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 1549 through 1551 698 hydrogen bonds defined for protein. 2052 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: 1.65 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1543 1.31 - 1.43: 2702 1.43 - 1.56: 5567 1.56 - 1.68: 7 1.68 - 1.81: 53 Bond restraints: 9872 Sorted by residual: bond pdb=" O5 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.448 1.648 -0.200 2.00e-02 2.50e+03 9.97e+01 bond pdb=" O4 GBM C1601 " pdb=" S2 GBM C1601 " ideal model delta sigma weight residual 1.453 1.647 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C4 ATP C1602 " pdb=" C5 ATP C1602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C5 ATP C1602 " pdb=" C6 ATP C1602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 bond pdb=" C17 GBM C1601 " pdb=" N8 GBM C1601 " ideal model delta sigma weight residual 1.340 1.443 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 9867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 13477 4.44 - 8.88: 84 8.88 - 13.32: 12 13.32 - 17.76: 1 17.76 - 22.20: 2 Bond angle restraints: 13576 Sorted by residual: angle pdb=" PB ATP C1602 " pdb=" O3B ATP C1602 " pdb=" PG ATP C1602 " ideal model delta sigma weight residual 139.87 117.67 22.20 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PA ATP C1602 " pdb=" O3A ATP C1602 " pdb=" PB ATP C1602 " ideal model delta sigma weight residual 136.83 117.58 19.25 1.00e+00 1.00e+00 3.70e+02 angle pdb=" C5 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N3 ATP C1602 " ideal model delta sigma weight residual 126.80 119.13 7.67 1.00e+00 1.00e+00 5.88e+01 angle pdb=" C LEU C 571 " pdb=" N SER C 572 " pdb=" CA SER C 572 " ideal model delta sigma weight residual 121.70 134.37 -12.67 1.80e+00 3.09e-01 4.95e+01 angle pdb=" N3 ATP C1602 " pdb=" C4 ATP C1602 " pdb=" N9 ATP C1602 " ideal model delta sigma weight residual 127.04 135.10 -8.06 1.15e+00 7.59e-01 4.93e+01 ... (remaining 13571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 5444 16.79 - 33.58: 219 33.58 - 50.37: 47 50.37 - 67.16: 6 67.16 - 83.95: 5 Dihedral angle restraints: 5721 sinusoidal: 1521 harmonic: 4200 Sorted by residual: dihedral pdb=" CA LYS C 252 " pdb=" C LYS C 252 " pdb=" N LEU C 253 " pdb=" CA LEU C 253 " ideal model delta harmonic sigma weight residual 180.00 132.03 47.97 0 5.00e+00 4.00e-02 9.20e+01 dihedral pdb=" CA ILE C 996 " pdb=" C ILE C 996 " pdb=" N PRO C 997 " pdb=" CA PRO C 997 " ideal model delta harmonic sigma weight residual -180.00 -137.86 -42.14 0 5.00e+00 4.00e-02 7.10e+01 dihedral pdb=" CA LYS C1562 " pdb=" C LYS C1562 " pdb=" N PRO C1563 " pdb=" CA PRO C1563 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 5718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1144 0.056 - 0.111: 416 0.111 - 0.167: 75 0.167 - 0.222: 7 0.222 - 0.278: 4 Chirality restraints: 1646 Sorted by residual: chirality pdb=" CG LEU C1248 " pdb=" CB LEU C1248 " pdb=" CD1 LEU C1248 " pdb=" CD2 LEU C1248 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU C 175 " pdb=" N LEU C 175 " pdb=" C LEU C 175 " pdb=" CB LEU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C1' ATP C1602 " pdb=" C2' ATP C1602 " pdb=" N9 ATP C1602 " pdb=" O4' ATP C1602 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1643 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 420 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU C 420 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU C 420 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL C 421 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 441 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO C 442 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1037 " 0.023 2.00e-02 2.50e+03 1.62e-02 6.53e+00 pdb=" CG TRP C1037 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C1037 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1037 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C1037 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1037 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1037 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C1037 " 0.000 2.00e-02 2.50e+03 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2259 2.78 - 3.31: 9152 3.31 - 3.84: 15453 3.84 - 4.37: 16243 4.37 - 4.90: 28403 Nonbonded interactions: 71510 Sorted by model distance: nonbonded pdb=" OH TYR C 123 " pdb=" O LEU C 135 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP C1128 " pdb=" NH1 ARG C1314 " model vdw 2.271 3.120 nonbonded pdb=" O GLU C 791 " pdb=" OH TYR C1219 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 338 " pdb=" O PHE C 345 " model vdw 2.291 3.040 nonbonded pdb=" O THR C 789 " pdb=" OG SER C 792 " model vdw 2.308 3.040 ... (remaining 71505 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.460 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 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 : 0.008 0.200 9873 Z= 0.366 Angle : 1.063 22.204 13578 Z= 0.612 Chirality : 0.058 0.278 1646 Planarity : 0.008 0.065 1752 Dihedral : 11.133 83.951 2988 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -4.29 (0.17), residues: 1429 helix: -2.33 (0.12), residues: 915 sheet: -3.78 (0.52), residues: 60 loop : -3.46 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C1145 TYR 0.033 0.003 TYR C 179 PHE 0.040 0.003 PHE C 432 TRP 0.044 0.003 TRP C1037 HIS 0.012 0.002 HIS C1098 Details of bonding type rmsd covalent geometry : bond 0.00778 ( 9872) covalent geometry : angle 1.06294 (13576) SS BOND : bond 0.01063 ( 1) SS BOND : angle 0.42519 ( 2) hydrogen bonds : bond 0.22645 ( 698) hydrogen bonds : angle 7.81561 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: C 112 MET cc_start: 0.6739 (mtm) cc_final: 0.6411 (mtp) REVERT: C 301 LEU cc_start: 0.6998 (tp) cc_final: 0.6398 (tt) REVERT: C 393 THR cc_start: 0.5310 (m) cc_final: 0.5049 (t) REVERT: C 1163 VAL cc_start: 0.6894 (t) cc_final: 0.6651 (t) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.0954 time to fit residues: 29.4725 Evaluate side-chains 144 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 262 ASN C 374 GLN C 397 ASN C 427 GLN C 707 GLN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 GLN C1245 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112098 restraints weight = 18317.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114812 restraints weight = 8639.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116612 restraints weight = 5113.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117764 restraints weight = 3560.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.118405 restraints weight = 2770.787| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9873 Z= 0.232 Angle : 0.768 10.660 13578 Z= 0.402 Chirality : 0.046 0.287 1646 Planarity : 0.006 0.061 1752 Dihedral : 7.023 75.819 1561 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.32 % Allowed : 12.97 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % Twisted General : 0.07 % 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: -2.00 (0.21), residues: 1429 helix: -0.26 (0.16), residues: 917 sheet: -3.71 (0.52), residues: 64 loop : -3.14 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 289 TYR 0.037 0.003 TYR C 123 PHE 0.024 0.003 PHE C 432 TRP 0.018 0.002 TRP C 65 HIS 0.008 0.001 HIS C 867 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9872) covalent geometry : angle 0.76825 (13576) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.20840 ( 2) hydrogen bonds : bond 0.05521 ( 698) hydrogen bonds : angle 4.72867 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7403 (tp) REVERT: C 257 MET cc_start: 0.8699 (mpp) cc_final: 0.8137 (mpp) REVERT: C 285 ARG cc_start: 0.6875 (tpt170) cc_final: 0.6673 (tpt170) outliers start: 30 outliers final: 17 residues processed: 209 average time/residue: 0.0881 time to fit residues: 26.5205 Evaluate side-chains 172 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 435 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1272 LEU Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 30.0000 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 8.9990 overall best weight: 1.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN C 105 HIS C 125 HIS C 219 GLN C 397 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1203 HIS C1234 ASN C1245 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.137109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113010 restraints weight = 18401.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115822 restraints weight = 8851.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117693 restraints weight = 5315.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118939 restraints weight = 3737.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119548 restraints weight = 2929.290| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9873 Z= 0.131 Angle : 0.627 9.173 13578 Z= 0.314 Chirality : 0.042 0.196 1646 Planarity : 0.005 0.071 1752 Dihedral : 6.554 74.117 1561 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.90 % Allowed : 18.01 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.71 (0.22), residues: 1429 helix: 0.79 (0.17), residues: 927 sheet: -3.44 (0.53), residues: 64 loop : -2.78 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1246 TYR 0.018 0.002 TYR C 230 PHE 0.016 0.002 PHE C 432 TRP 0.013 0.001 TRP C 430 HIS 0.006 0.001 HIS C 867 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9872) covalent geometry : angle 0.62664 (13576) SS BOND : bond 0.00296 ( 1) SS BOND : angle 1.61125 ( 2) hydrogen bonds : bond 0.04783 ( 698) hydrogen bonds : angle 4.03344 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7009 (tp) REVERT: C 770 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7807 (p) REVERT: C 1030 ILE cc_start: 0.7512 (tp) cc_final: 0.7047 (pt) outliers start: 34 outliers final: 20 residues processed: 191 average time/residue: 0.0831 time to fit residues: 23.5664 Evaluate side-chains 177 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1154 LEU Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1245 ASN Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 140 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 130 optimal weight: 40.0000 chunk 41 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 58 optimal weight: 0.0770 chunk 141 optimal weight: 20.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.109820 restraints weight = 18708.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112509 restraints weight = 9062.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114349 restraints weight = 5521.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115333 restraints weight = 3933.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116280 restraints weight = 3208.175| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9873 Z= 0.201 Angle : 0.713 10.128 13578 Z= 0.374 Chirality : 0.045 0.202 1646 Planarity : 0.006 0.070 1752 Dihedral : 6.460 74.932 1561 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 7.20 % Allowed : 17.87 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.44 (0.22), residues: 1429 helix: 0.95 (0.17), residues: 922 sheet: -3.50 (0.58), residues: 50 loop : -2.55 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1218 TYR 0.042 0.003 TYR C1064 PHE 0.050 0.002 PHE C 433 TRP 0.044 0.003 TRP C1033 HIS 0.010 0.001 HIS C1203 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9872) covalent geometry : angle 0.71214 (13576) SS BOND : bond 0.00573 ( 1) SS BOND : angle 2.63992 ( 2) hydrogen bonds : bond 0.05130 ( 698) hydrogen bonds : angle 4.08770 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7579 (tp) REVERT: C 158 TYR cc_start: 0.6879 (t80) cc_final: 0.6470 (t80) REVERT: C 424 ASP cc_start: 0.6767 (m-30) cc_final: 0.6487 (m-30) REVERT: C 426 ASN cc_start: 0.8536 (t0) cc_final: 0.8283 (t0) REVERT: C 531 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7437 (p) outliers start: 50 outliers final: 30 residues processed: 214 average time/residue: 0.0838 time to fit residues: 26.2531 Evaluate side-chains 193 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1192 LEU Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1298 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN C 427 GLN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104402 restraints weight = 18933.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.106994 restraints weight = 9528.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108741 restraints weight = 5912.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.109885 restraints weight = 4314.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110287 restraints weight = 3476.387| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.9166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9873 Z= 0.224 Angle : 0.711 10.013 13578 Z= 0.370 Chirality : 0.046 0.284 1646 Planarity : 0.005 0.062 1752 Dihedral : 6.785 70.887 1561 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 7.93 % Allowed : 20.17 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: -0.38 (0.22), residues: 1429 helix: 1.00 (0.17), residues: 927 sheet: -3.60 (0.59), residues: 51 loop : -2.54 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C1187 TYR 0.023 0.002 TYR C 263 PHE 0.023 0.002 PHE C1182 TRP 0.021 0.002 TRP C 288 HIS 0.008 0.002 HIS C 584 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 9872) covalent geometry : angle 0.71075 (13576) SS BOND : bond 0.00825 ( 1) SS BOND : angle 2.40607 ( 2) hydrogen bonds : bond 0.05149 ( 698) hydrogen bonds : angle 4.26798 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8190 (tp) REVERT: C 108 MET cc_start: 0.7856 (mmp) cc_final: 0.7568 (tpp) REVERT: C 158 TYR cc_start: 0.7250 (t80) cc_final: 0.6693 (t80) REVERT: C 426 ASN cc_start: 0.8802 (t0) cc_final: 0.8552 (t0) REVERT: C 528 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7613 (mtpt) REVERT: C 574 SER cc_start: 0.7711 (p) cc_final: 0.7387 (p) REVERT: C 1025 MET cc_start: 0.7988 (tpp) cc_final: 0.7706 (mmp) REVERT: C 1091 LEU cc_start: 0.8633 (tp) cc_final: 0.8229 (tt) REVERT: C 1229 GLU cc_start: 0.8176 (tp30) cc_final: 0.7906 (tm-30) outliers start: 55 outliers final: 38 residues processed: 203 average time/residue: 0.0816 time to fit residues: 24.5545 Evaluate side-chains 187 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1038 THR Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1139 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1173 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1253 GLU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1283 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 73 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 84 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 overall best weight: 1.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 293 HIS C 444 GLN C 485 GLN C 491 HIS C 547 ASN C 896 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107949 restraints weight = 18585.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110612 restraints weight = 9127.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.112406 restraints weight = 5613.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.113620 restraints weight = 4053.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114162 restraints weight = 3239.565| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.9492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9873 Z= 0.133 Angle : 0.612 9.006 13578 Z= 0.310 Chirality : 0.043 0.312 1646 Planarity : 0.005 0.060 1752 Dihedral : 6.356 70.314 1561 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.19 % Allowed : 27.23 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.30 (0.23), residues: 1429 helix: 1.54 (0.17), residues: 927 sheet: -3.39 (0.61), residues: 51 loop : -2.29 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 289 TYR 0.018 0.002 TYR C 142 PHE 0.023 0.001 PHE C 41 TRP 0.017 0.001 TRP C1297 HIS 0.011 0.002 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9872) covalent geometry : angle 0.61215 (13576) SS BOND : bond 0.00391 ( 1) SS BOND : angle 1.33358 ( 2) hydrogen bonds : bond 0.04294 ( 698) hydrogen bonds : angle 3.81927 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7025 (mpp) cc_final: 0.6814 (mpp) REVERT: C 54 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: C 80 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8100 (tp) REVERT: C 158 TYR cc_start: 0.7162 (t80) cc_final: 0.6625 (t80) REVERT: C 370 ARG cc_start: 0.7655 (mmt90) cc_final: 0.7406 (mmt90) REVERT: C 426 ASN cc_start: 0.8750 (t0) cc_final: 0.8435 (m-40) REVERT: C 574 SER cc_start: 0.7516 (p) cc_final: 0.7199 (p) REVERT: C 577 PHE cc_start: 0.8003 (m-80) cc_final: 0.7723 (m-80) REVERT: C 1025 MET cc_start: 0.7919 (tpp) cc_final: 0.7633 (mmp) REVERT: C 1038 THR cc_start: 0.8021 (t) cc_final: 0.7733 (t) REVERT: C 1091 LEU cc_start: 0.8666 (tp) cc_final: 0.8298 (tt) REVERT: C 1229 GLU cc_start: 0.8204 (tp30) cc_final: 0.7896 (tm-30) REVERT: C 1305 MET cc_start: 0.7920 (tmm) cc_final: 0.7657 (tpp) outliers start: 36 outliers final: 20 residues processed: 183 average time/residue: 0.0867 time to fit residues: 23.2746 Evaluate side-chains 167 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 30.0000 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 134 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107444 restraints weight = 18598.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110123 restraints weight = 9141.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111907 restraints weight = 5614.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.113012 restraints weight = 4065.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113761 restraints weight = 3285.479| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.9700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9873 Z= 0.136 Angle : 0.619 9.415 13578 Z= 0.314 Chirality : 0.043 0.261 1646 Planarity : 0.005 0.072 1752 Dihedral : 6.259 71.705 1561 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.03 % Allowed : 28.82 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.53 (0.23), residues: 1429 helix: 1.71 (0.17), residues: 927 sheet: -3.36 (0.62), residues: 51 loop : -2.20 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 289 TYR 0.016 0.002 TYR C 142 PHE 0.034 0.001 PHE C1164 TRP 0.025 0.001 TRP C1297 HIS 0.019 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9872) covalent geometry : angle 0.61870 (13576) SS BOND : bond 0.00442 ( 1) SS BOND : angle 1.40262 ( 2) hydrogen bonds : bond 0.04225 ( 698) hydrogen bonds : angle 3.77607 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7006 (mpp) cc_final: 0.6763 (mpp) REVERT: C 54 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: C 80 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 108 MET cc_start: 0.8496 (tpp) cc_final: 0.8036 (tpp) REVERT: C 158 TYR cc_start: 0.7138 (t80) cc_final: 0.6614 (t80) REVERT: C 257 MET cc_start: 0.8691 (mpp) cc_final: 0.8367 (mtt) REVERT: C 426 ASN cc_start: 0.8720 (t0) cc_final: 0.8456 (m-40) REVERT: C 574 SER cc_start: 0.7525 (p) cc_final: 0.7147 (p) REVERT: C 577 PHE cc_start: 0.8022 (m-80) cc_final: 0.7729 (m-80) REVERT: C 1025 MET cc_start: 0.7864 (tpp) cc_final: 0.7608 (mmp) REVERT: C 1091 LEU cc_start: 0.8688 (tp) cc_final: 0.8277 (tt) REVERT: C 1227 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8707 (tp) REVERT: C 1229 GLU cc_start: 0.8236 (tp30) cc_final: 0.7922 (tm-30) REVERT: C 1230 TYR cc_start: 0.8756 (m-80) cc_final: 0.8496 (m-80) REVERT: C 1305 MET cc_start: 0.7859 (tmm) cc_final: 0.7618 (tpp) outliers start: 28 outliers final: 21 residues processed: 172 average time/residue: 0.0870 time to fit residues: 21.8502 Evaluate side-chains 175 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 39 optimal weight: 6.9990 chunk 134 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 141 optimal weight: 50.0000 chunk 84 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 127 optimal weight: 5.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 HIS C 293 HIS C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102113 restraints weight = 19015.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104642 restraints weight = 9704.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106294 restraints weight = 6122.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107422 restraints weight = 4488.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.107973 restraints weight = 3654.837| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 1.0454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9873 Z= 0.205 Angle : 0.688 9.324 13578 Z= 0.355 Chirality : 0.045 0.220 1646 Planarity : 0.005 0.078 1752 Dihedral : 6.557 74.542 1561 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.48 % Allowed : 26.37 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.27 (0.23), residues: 1429 helix: 1.50 (0.17), residues: 928 sheet: -3.61 (0.61), residues: 51 loop : -2.24 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 289 TYR 0.014 0.002 TYR C 142 PHE 0.021 0.002 PHE C1164 TRP 0.022 0.002 TRP C1297 HIS 0.011 0.002 HIS C 491 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9872) covalent geometry : angle 0.68755 (13576) SS BOND : bond 0.00834 ( 1) SS BOND : angle 2.24991 ( 2) hydrogen bonds : bond 0.04814 ( 698) hydrogen bonds : angle 4.02045 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7318 (mpp) cc_final: 0.7115 (mpp) REVERT: C 54 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6598 (mp10) REVERT: C 80 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8458 (tp) REVERT: C 88 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 158 TYR cc_start: 0.7387 (t80) cc_final: 0.6782 (t80) REVERT: C 227 LYS cc_start: 0.9421 (mttt) cc_final: 0.9025 (mtmm) REVERT: C 289 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8404 (mtm-85) REVERT: C 426 ASN cc_start: 0.8818 (t0) cc_final: 0.8489 (m-40) REVERT: C 574 SER cc_start: 0.7858 (p) cc_final: 0.7513 (p) REVERT: C 1025 MET cc_start: 0.7954 (tpp) cc_final: 0.7710 (mmp) REVERT: C 1091 LEU cc_start: 0.8820 (tp) cc_final: 0.8367 (tt) REVERT: C 1229 GLU cc_start: 0.8265 (tp30) cc_final: 0.7953 (tm-30) REVERT: C 1305 MET cc_start: 0.7999 (tmm) cc_final: 0.7748 (tpp) outliers start: 45 outliers final: 35 residues processed: 191 average time/residue: 0.0885 time to fit residues: 24.2521 Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 241 HIS C 293 HIS C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102534 restraints weight = 18918.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105209 restraints weight = 9249.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106973 restraints weight = 5645.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108107 restraints weight = 4053.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108595 restraints weight = 3250.388| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 1.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9873 Z= 0.183 Angle : 0.653 9.356 13578 Z= 0.337 Chirality : 0.044 0.198 1646 Planarity : 0.005 0.068 1752 Dihedral : 6.473 74.084 1561 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.91 % Allowed : 28.10 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.39 (0.23), residues: 1429 helix: 1.59 (0.17), residues: 929 sheet: -3.67 (0.61), residues: 51 loop : -2.18 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 289 TYR 0.015 0.002 TYR C 396 PHE 0.019 0.001 PHE C 433 TRP 0.028 0.002 TRP C 899 HIS 0.010 0.002 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9872) covalent geometry : angle 0.65281 (13576) SS BOND : bond 0.00707 ( 1) SS BOND : angle 1.83012 ( 2) hydrogen bonds : bond 0.04572 ( 698) hydrogen bonds : angle 3.93346 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 PHE cc_start: 0.7814 (m-80) cc_final: 0.7595 (t80) REVERT: C 54 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6415 (mp10) REVERT: C 88 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7458 (mm-30) REVERT: C 158 TYR cc_start: 0.7503 (t80) cc_final: 0.6848 (t80) REVERT: C 257 MET cc_start: 0.8759 (mpp) cc_final: 0.8491 (mtt) REVERT: C 285 ARG cc_start: 0.6700 (tpt170) cc_final: 0.6227 (tpt170) REVERT: C 289 ARG cc_start: 0.8719 (mtt90) cc_final: 0.8302 (mtm-85) REVERT: C 426 ASN cc_start: 0.8740 (t0) cc_final: 0.8456 (m-40) REVERT: C 574 SER cc_start: 0.7862 (p) cc_final: 0.7476 (p) REVERT: C 577 PHE cc_start: 0.8206 (m-80) cc_final: 0.7944 (m-80) REVERT: C 1025 MET cc_start: 0.8004 (tpp) cc_final: 0.7681 (mmp) REVERT: C 1229 GLU cc_start: 0.8307 (tp30) cc_final: 0.7989 (tm-30) REVERT: C 1230 TYR cc_start: 0.8815 (m-80) cc_final: 0.8611 (m-80) outliers start: 41 outliers final: 38 residues processed: 173 average time/residue: 0.0859 time to fit residues: 21.5900 Evaluate side-chains 185 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1155 THR Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1234 ASN Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1306 GLU Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS C 241 HIS C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104729 restraints weight = 18697.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107254 restraints weight = 9463.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108916 restraints weight = 5931.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110034 restraints weight = 4317.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110534 restraints weight = 3484.837| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 1.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9873 Z= 0.140 Angle : 0.623 9.252 13578 Z= 0.318 Chirality : 0.043 0.205 1646 Planarity : 0.005 0.059 1752 Dihedral : 6.368 74.271 1561 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.19 % Allowed : 28.67 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.57 (0.24), residues: 1429 helix: 1.72 (0.17), residues: 934 sheet: -3.64 (0.61), residues: 51 loop : -2.15 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 289 TYR 0.026 0.002 TYR C 845 PHE 0.026 0.001 PHE C1164 TRP 0.028 0.001 TRP C 899 HIS 0.019 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9872) covalent geometry : angle 0.62308 (13576) SS BOND : bond 0.00520 ( 1) SS BOND : angle 1.50683 ( 2) hydrogen bonds : bond 0.04341 ( 698) hydrogen bonds : angle 3.81381 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: C 88 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7383 (mm-30) REVERT: C 158 TYR cc_start: 0.7365 (t80) cc_final: 0.6761 (t80) REVERT: C 257 MET cc_start: 0.8650 (mpp) cc_final: 0.8428 (mtt) REVERT: C 426 ASN cc_start: 0.8735 (t0) cc_final: 0.8433 (m-40) REVERT: C 574 SER cc_start: 0.7750 (p) cc_final: 0.7353 (p) REVERT: C 577 PHE cc_start: 0.8157 (m-80) cc_final: 0.7931 (m-80) REVERT: C 1025 MET cc_start: 0.7933 (tpp) cc_final: 0.7649 (mmp) REVERT: C 1038 THR cc_start: 0.8011 (t) cc_final: 0.7747 (t) REVERT: C 1229 GLU cc_start: 0.8272 (tp30) cc_final: 0.7953 (tm-30) outliers start: 36 outliers final: 31 residues processed: 170 average time/residue: 0.0822 time to fit residues: 20.6632 Evaluate side-chains 179 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 491 HIS Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 770 VAL Chi-restraints excluded: chain C residue 1018 PHE Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1096 ARG Chi-restraints excluded: chain C residue 1136 ILE Chi-restraints excluded: chain C residue 1157 ILE Chi-restraints excluded: chain C residue 1158 SER Chi-restraints excluded: chain C residue 1165 LEU Chi-restraints excluded: chain C residue 1219 TYR Chi-restraints excluded: chain C residue 1227 LEU Chi-restraints excluded: chain C residue 1234 ASN Chi-restraints excluded: chain C residue 1242 THR Chi-restraints excluded: chain C residue 1283 LEU Chi-restraints excluded: chain C residue 1296 ASN Chi-restraints excluded: chain C residue 1307 ILE Chi-restraints excluded: chain C residue 1315 ILE Chi-restraints excluded: chain C residue 1325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 40.0000 chunk 131 optimal weight: 0.0020 chunk 139 optimal weight: 0.0050 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 40.0000 chunk 114 optimal weight: 3.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105870 restraints weight = 18732.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108545 restraints weight = 9103.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110351 restraints weight = 5581.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111464 restraints weight = 4020.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112122 restraints weight = 3242.933| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 1.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9873 Z= 0.125 Angle : 0.610 9.174 13578 Z= 0.310 Chirality : 0.042 0.203 1646 Planarity : 0.005 0.059 1752 Dihedral : 6.222 75.096 1561 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.18 % Allowed : 29.83 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 2.04 % 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: 0.76 (0.24), residues: 1429 helix: 1.88 (0.17), residues: 935 sheet: -3.59 (0.62), residues: 51 loop : -2.08 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1300 TYR 0.029 0.002 TYR C 845 PHE 0.028 0.001 PHE C1164 TRP 0.026 0.001 TRP C 899 HIS 0.021 0.002 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9872) covalent geometry : angle 0.61023 (13576) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.13437 ( 2) hydrogen bonds : bond 0.04107 ( 698) hydrogen bonds : angle 3.70091 ( 2052) =============================================================================== Job complete usr+sys time: 1639.77 seconds wall clock time: 28 minutes 49.76 seconds (1729.76 seconds total)