Starting phenix.real_space_refine on Wed Feb 4 14:19:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgf_63064/02_2026/9lgf_63064.map" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.089 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 6 5.49 5 Mg 2 5.21 5 S 57 5.16 5 C 7027 2.51 5 N 1798 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10828 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 10764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1355, 10764 Classifications: {'peptide': 1355} Link IDs: {'PTRANS': 48, 'TRANS': 1306} Chain breaks: 10 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.73, per 1000 atoms: 0.25 Number of scatterers: 10828 At special positions: 0 Unit cell: (74, 107, 145, 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) S 57 16.00 P 6 15.00 Mg 2 11.99 O 1938 8.00 N 1798 7.00 C 7027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 510.5 milliseconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 71.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.654A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 60 removed outlier: 3.959A pdb=" N LEU B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL B 39 " --> pdb=" O ASN B 35 " (cutoff:3.500A) Proline residue: B 42 - end of helix Proline residue: B 51 - end of helix removed outlier: 3.867A pdb=" N LEU B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.697A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 130 removed outlier: 3.577A pdb=" N VAL B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 135 through 160 Processing helix chain 'B' and resid 171 through 191 removed outlier: 3.544A pdb=" N PHE B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 224 through 234 Processing helix chain 'B' and resid 249 through 269 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 312 through 326 removed outlier: 3.746A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 326 through 353 removed outlier: 3.723A pdb=" N LEU B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 359 through 410 removed outlier: 3.925A pdb=" N GLY B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.609A pdb=" N PHE B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 439 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 462 removed outlier: 3.560A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Proline residue: B 448 - end of helix Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 466 through 511 removed outlier: 3.649A pdb=" N VAL B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) Proline residue: B 478 - end of helix Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 520 through 570 Proline residue: B 557 - end of helix removed outlier: 3.803A pdb=" N THR B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 621 removed outlier: 3.556A pdb=" N SER B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Proline residue: B 595 - end of helix Proline residue: B 600 - end of helix Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 733 through 744 removed outlier: 3.516A pdb=" N ALA B 739 " --> pdb=" O ARG B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 769 through 784 Processing helix chain 'B' and resid 799 through 810 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 860 through 869 Processing helix chain 'B' and resid 958 through 970 removed outlier: 3.845A pdb=" N TYR B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 997 removed outlier: 3.573A pdb=" N LEU B 997 " --> pdb=" O TYR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1014 Processing helix chain 'B' and resid 1014 through 1058 removed outlier: 3.616A pdb=" N THR B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1037 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B1038 " --> pdb=" O MET B1034 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B1049 " --> pdb=" O ARG B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1066 removed outlier: 3.551A pdb=" N PHE B1063 " --> pdb=" O PRO B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1077 through 1084 Processing helix chain 'B' and resid 1084 through 1110 removed outlier: 3.534A pdb=" N GLN B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1116 removed outlier: 3.647A pdb=" N VAL B1116 " --> pdb=" O MET B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1160 removed outlier: 4.297A pdb=" N SER B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLN B1138 " --> pdb=" O ALA B1134 " (cutoff:3.500A) Proline residue: B1149 - end of helix Processing helix chain 'B' and resid 1160 through 1168 Processing helix chain 'B' and resid 1169 through 1220 Proline residue: B1190 - end of helix removed outlier: 4.443A pdb=" N PHE B1212 " --> pdb=" O CYS B1208 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B1220 " --> pdb=" O PHE B1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1264 removed outlier: 3.763A pdb=" N SER B1234 " --> pdb=" O GLY B1230 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B1238 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B1258 " --> pdb=" O GLU B1254 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B1260 " --> pdb=" O ASN B1256 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1267 No H-bonds generated for 'chain 'B' and resid 1265 through 1267' Processing helix chain 'B' and resid 1331 through 1340 removed outlier: 3.648A pdb=" N THR B1336 " --> pdb=" O LYS B1332 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1367 Processing helix chain 'B' and resid 1383 through 1388 Processing helix chain 'B' and resid 1394 through 1404 Processing helix chain 'B' and resid 1407 through 1414 Processing helix chain 'B' and resid 1416 through 1419 Processing helix chain 'B' and resid 1423 through 1427 removed outlier: 3.951A pdb=" N GLU B1427 " --> pdb=" O GLU B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1430 through 1446 Processing helix chain 'B' and resid 1460 through 1475 Processing helix chain 'B' and resid 1486 through 1490 Processing helix chain 'B' and resid 1509 through 1517 Processing helix chain 'B' and resid 1518 through 1527 Processing sheet with id=AA1, first strand: chain 'B' and resid 630 through 631 removed outlier: 5.925A pdb=" N GLN B 631 " --> pdb=" O VAL B 704 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILE B 664 " --> pdb=" O ASN B 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 651 through 652 Processing sheet with id=AA3, first strand: chain 'B' and resid 708 through 711 removed outlier: 6.585A pdb=" N TYR B 789 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 825 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 791 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 674 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 673 " --> pdb=" O VAL B 837 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 839 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA B 675 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET B 841 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 677 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 848 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER B 842 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE B 846 " --> pdb=" O SER B 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1298 through 1299 Processing sheet with id=AA5, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 7.020A pdb=" N VAL B1322 " --> pdb=" O THR B1482 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS B1321 " --> pdb=" O ARG B1495 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE B1497 " --> pdb=" O LYS B1321 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY B1323 " --> pdb=" O ILE B1497 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B1499 " --> pdb=" O GLY B1323 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B1325 " --> pdb=" O LEU B1499 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B1506 " --> pdb=" O VAL B1498 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1351 through 1352 Processing sheet with id=AA7, first strand: chain 'B' and resid 1381 through 1382 699 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: 2.14 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1698 1.31 - 1.44: 2984 1.44 - 1.56: 6282 1.56 - 1.69: 10 1.69 - 1.81: 93 Bond restraints: 11067 Sorted by residual: bond pdb=" CA ALA B1217 " pdb=" CB ALA B1217 " ideal model delta sigma weight residual 1.532 1.470 0.062 1.65e-02 3.67e+03 1.39e+01 bond pdb=" C GLU B1261 " pdb=" O GLU B1261 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.29e-02 6.01e+03 1.38e+01 bond pdb=" C PHE B 975 " pdb=" O PHE B 975 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" N PRO B 478 " pdb=" CD PRO B 478 " ideal model delta sigma weight residual 1.473 1.523 -0.050 1.40e-02 5.10e+03 1.26e+01 bond pdb=" N PHE B 594 " pdb=" CA PHE B 594 " ideal model delta sigma weight residual 1.463 1.487 -0.024 6.90e-03 2.10e+04 1.21e+01 ... (remaining 11062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 14066 2.04 - 4.07: 913 4.07 - 6.11: 44 6.11 - 8.15: 7 8.15 - 10.18: 3 Bond angle restraints: 15033 Sorted by residual: angle pdb=" PB ATP B1603 " pdb=" O3B ATP B1603 " pdb=" PG ATP B1603 " ideal model delta sigma weight residual 139.87 131.31 8.56 1.00e+00 1.00e+00 7.33e+01 angle pdb=" PB ATP B1601 " pdb=" O3B ATP B1601 " pdb=" PG ATP B1601 " ideal model delta sigma weight residual 139.87 132.42 7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" PA ATP B1603 " pdb=" O3A ATP B1603 " pdb=" PB ATP B1603 " ideal model delta sigma weight residual 136.83 130.86 5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" N CYS B1208 " pdb=" CA CYS B1208 " pdb=" C CYS B1208 " ideal model delta sigma weight residual 112.59 105.43 7.16 1.22e+00 6.72e-01 3.45e+01 angle pdb=" N ILE B1219 " pdb=" CA ILE B1219 " pdb=" C ILE B1219 " ideal model delta sigma weight residual 113.16 104.91 8.25 1.49e+00 4.50e-01 3.07e+01 ... (remaining 15028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 5722 16.03 - 32.05: 618 32.05 - 48.08: 172 48.08 - 64.10: 74 64.10 - 80.13: 15 Dihedral angle restraints: 6601 sinusoidal: 2645 harmonic: 3956 Sorted by residual: dihedral pdb=" CA VAL B 429 " pdb=" C VAL B 429 " pdb=" N ASP B 430 " pdb=" CA ASP B 430 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP B1395 " pdb=" CB ASP B1395 " pdb=" CG ASP B1395 " pdb=" OD1 ASP B1395 " ideal model delta sinusoidal sigma weight residual -30.00 -89.13 59.13 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B1375 " pdb=" CB ASP B1375 " pdb=" CG ASP B1375 " pdb=" OD1 ASP B1375 " ideal model delta sinusoidal sigma weight residual -30.00 -87.78 57.78 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1289 0.061 - 0.122: 317 0.122 - 0.184: 122 0.184 - 0.245: 19 0.245 - 0.306: 3 Chirality restraints: 1750 Sorted by residual: chirality pdb=" CA ILE B 576 " pdb=" N ILE B 576 " pdb=" C ILE B 576 " pdb=" CB ILE B 576 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE B1504 " pdb=" N ILE B1504 " pdb=" C ILE B1504 " pdb=" CB ILE B1504 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE B1209 " pdb=" N ILE B1209 " pdb=" C ILE B1209 " pdb=" CB ILE B1209 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1747 not shown) Planarity restraints: 1845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 461 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C ASN B 461 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN B 461 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 462 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1196 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.89e+00 pdb=" NE ARG B1196 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B1196 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B1196 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B1196 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 560 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C VAL B 560 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 560 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA B 561 " -0.017 2.00e-02 2.50e+03 ... (remaining 1842 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 13 2.34 - 2.98: 5808 2.98 - 3.62: 17131 3.62 - 4.26: 25755 4.26 - 4.90: 44137 Nonbonded interactions: 92844 Sorted by model distance: nonbonded pdb=" OE1 GLN B1374 " pdb="MG MG B1604 " model vdw 1.702 2.170 nonbonded pdb=" O3G ATP B1603 " pdb="MG MG B1604 " model vdw 2.011 2.170 nonbonded pdb=" OG SER B1333 " pdb="MG MG B1604 " model vdw 2.069 2.170 nonbonded pdb=" OG SER B 685 " pdb="MG MG B1602 " model vdw 2.084 2.170 nonbonded pdb=" OE1 GLN B 713 " pdb="MG MG B1602 " model vdw 2.243 2.170 ... (remaining 92839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.220 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11067 Z= 0.517 Angle : 0.928 10.182 15033 Z= 0.684 Chirality : 0.065 0.306 1750 Planarity : 0.007 0.120 1845 Dihedral : 15.972 80.129 4035 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.25 % Allowed : 17.02 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1333 helix: 0.21 (0.17), residues: 871 sheet: -0.51 (0.97), residues: 29 loop : -1.23 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 858 TYR 0.017 0.001 TYR B1297 PHE 0.025 0.002 PHE B 175 TRP 0.012 0.001 TRP B 361 HIS 0.006 0.001 HIS B 985 Details of bonding type rmsd covalent geometry : bond 0.00717 (11067) covalent geometry : angle 0.92776 (15033) hydrogen bonds : bond 0.17060 ( 699) hydrogen bonds : angle 7.10952 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 270 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.7891 (tt0) cc_final: 0.7310 (tp40) REVERT: B 262 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7540 (mtpt) REVERT: B 345 ILE cc_start: 0.8159 (mm) cc_final: 0.7947 (mp) REVERT: B 382 HIS cc_start: 0.7135 (m170) cc_final: 0.6768 (m-70) REVERT: B 459 TRP cc_start: 0.7193 (t-100) cc_final: 0.6944 (t60) REVERT: B 485 MET cc_start: 0.6914 (mmt) cc_final: 0.6164 (mtm) REVERT: B 505 MET cc_start: 0.7159 (mmm) cc_final: 0.6839 (mmm) REVERT: B 533 GLN cc_start: 0.7295 (mm110) cc_final: 0.7073 (mm-40) REVERT: B 631 GLN cc_start: 0.7091 (mt0) cc_final: 0.6718 (mt0) REVERT: B 679 GLN cc_start: 0.6582 (pm20) cc_final: 0.5423 (mt0) REVERT: B 699 GLU cc_start: 0.6873 (pp20) cc_final: 0.6556 (pp20) REVERT: B 734 GLU cc_start: 0.7554 (tp30) cc_final: 0.7047 (mp0) REVERT: B 808 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7387 (mp0) REVERT: B 831 TYR cc_start: 0.7363 (m-80) cc_final: 0.7025 (m-10) REVERT: B 951 LYS cc_start: 0.7428 (ttpp) cc_final: 0.7014 (mptt) REVERT: B 966 MET cc_start: 0.7606 (mmt) cc_final: 0.7405 (mmt) REVERT: B 1088 GLN cc_start: 0.7561 (tt0) cc_final: 0.6794 (tp40) REVERT: B 1090 ILE cc_start: 0.8278 (mt) cc_final: 0.7872 (pt) REVERT: B 1216 PHE cc_start: 0.6964 (t80) cc_final: 0.6732 (t80) REVERT: B 1245 TRP cc_start: 0.6876 (m-10) cc_final: 0.6347 (m100) REVERT: B 1264 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6748 (mtpp) REVERT: B 1267 SER cc_start: 0.8799 (t) cc_final: 0.8561 (p) REVERT: B 1315 THR cc_start: 0.8055 (m) cc_final: 0.7689 (p) REVERT: B 1343 LYS cc_start: 0.8217 (tppt) cc_final: 0.7668 (mmmt) REVERT: B 1377 VAL cc_start: 0.7907 (p) cc_final: 0.7693 (p) REVERT: B 1523 MET cc_start: 0.7885 (mtp) cc_final: 0.7640 (mtp) outliers start: 3 outliers final: 1 residues processed: 273 average time/residue: 0.1292 time to fit residues: 48.2010 Evaluate side-chains 170 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 947 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS B 230 GLN B 377 GLN B 622 HIS B 701 HIS B1207 ASN ** B1363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.184698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147074 restraints weight = 12331.662| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.90 r_work: 0.3576 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11067 Z= 0.163 Angle : 0.567 7.903 15033 Z= 0.296 Chirality : 0.041 0.168 1750 Planarity : 0.004 0.048 1845 Dihedral : 8.222 83.593 1523 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.37 % Allowed : 16.93 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.23), residues: 1333 helix: 1.53 (0.17), residues: 884 sheet: -0.98 (0.98), residues: 28 loop : -0.85 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1165 TYR 0.032 0.002 TYR B1032 PHE 0.014 0.002 PHE B 175 TRP 0.008 0.001 TRP B1197 HIS 0.005 0.001 HIS B 494 Details of bonding type rmsd covalent geometry : bond 0.00367 (11067) covalent geometry : angle 0.56748 (15033) hydrogen bonds : bond 0.04466 ( 699) hydrogen bonds : angle 4.48024 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 262 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8087 (mtpt) REVERT: B 317 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 422 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 485 MET cc_start: 0.7827 (mmt) cc_final: 0.7225 (mtm) REVERT: B 505 MET cc_start: 0.8070 (mmm) cc_final: 0.7771 (mmm) REVERT: B 601 MET cc_start: 0.7721 (mtp) cc_final: 0.7492 (mpp) REVERT: B 626 ASP cc_start: 0.7527 (t0) cc_final: 0.7287 (t0) REVERT: B 631 GLN cc_start: 0.8017 (mt0) cc_final: 0.7694 (mt0) REVERT: B 679 GLN cc_start: 0.7528 (pm20) cc_final: 0.6897 (mt0) REVERT: B 734 GLU cc_start: 0.8190 (tp30) cc_final: 0.7604 (mp0) REVERT: B 808 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8117 (mm-30) REVERT: B 854 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7301 (tt0) REVERT: B 951 LYS cc_start: 0.7884 (ttpp) cc_final: 0.7590 (mptt) REVERT: B 991 SER cc_start: 0.7999 (t) cc_final: 0.7789 (p) REVERT: B 1085 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7707 (mpp) REVERT: B 1088 GLN cc_start: 0.8069 (tt0) cc_final: 0.7689 (tp-100) REVERT: B 1094 MET cc_start: 0.8367 (mmm) cc_final: 0.8085 (mmm) REVERT: B 1139 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8001 (mt) REVERT: B 1245 TRP cc_start: 0.7779 (m-10) cc_final: 0.7286 (m100) REVERT: B 1264 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7760 (mtpp) REVERT: B 1315 THR cc_start: 0.8370 (m) cc_final: 0.8142 (p) REVERT: B 1343 LYS cc_start: 0.8507 (tppt) cc_final: 0.8115 (mmmt) REVERT: B 1414 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7965 (mp) REVERT: B 1476 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6572 (m-30) outliers start: 40 outliers final: 13 residues processed: 211 average time/residue: 0.1115 time to fit residues: 33.6493 Evaluate side-chains 168 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1027 ILE Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1322 VAL Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 662 HIS B 701 HIS B 725 ASN B1155 ASN B1195 ASN B1363 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130321 restraints weight = 12114.469| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.87 r_work: 0.3374 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11067 Z= 0.170 Angle : 0.542 6.921 15033 Z= 0.285 Chirality : 0.041 0.155 1750 Planarity : 0.004 0.049 1845 Dihedral : 8.199 76.400 1522 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.45 % Allowed : 17.52 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1333 helix: 1.68 (0.17), residues: 883 sheet: -2.05 (1.11), residues: 22 loop : -0.81 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 775 TYR 0.025 0.002 TYR B1032 PHE 0.017 0.002 PHE B 589 TRP 0.009 0.001 TRP B1197 HIS 0.017 0.002 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00398 (11067) covalent geometry : angle 0.54226 (15033) hydrogen bonds : bond 0.04325 ( 699) hydrogen bonds : angle 4.21677 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 230 GLN cc_start: 0.8213 (tp40) cc_final: 0.7886 (tp40) REVERT: B 262 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7853 (mtpt) REVERT: B 422 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 485 MET cc_start: 0.7801 (mmt) cc_final: 0.7093 (mtm) REVERT: B 505 MET cc_start: 0.8123 (mmm) cc_final: 0.7729 (mmm) REVERT: B 679 GLN cc_start: 0.7403 (pm20) cc_final: 0.6797 (mt0) REVERT: B 734 GLU cc_start: 0.8123 (tp30) cc_final: 0.7668 (mp0) REVERT: B 804 LYS cc_start: 0.8280 (tttt) cc_final: 0.8074 (ttmm) REVERT: B 951 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7598 (mptt) REVERT: B 1085 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: B 1088 GLN cc_start: 0.8110 (tt0) cc_final: 0.7605 (tp-100) REVERT: B 1094 MET cc_start: 0.8389 (mmm) cc_final: 0.8158 (mmm) REVERT: B 1132 TYR cc_start: 0.8474 (t80) cc_final: 0.7379 (t80) REVERT: B 1139 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8202 (mm) REVERT: B 1264 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7644 (mtpp) REVERT: B 1343 LYS cc_start: 0.8349 (tppt) cc_final: 0.7926 (mmmt) REVERT: B 1414 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7999 (mp) REVERT: B 1476 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: B 1523 MET cc_start: 0.8706 (mtp) cc_final: 0.8415 (mtt) outliers start: 41 outliers final: 21 residues processed: 198 average time/residue: 0.1249 time to fit residues: 34.0805 Evaluate side-chains 181 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1198 LEU Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 35 optimal weight: 0.0670 chunk 57 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 767 ASN B1053 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.167490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131011 restraints weight = 12038.182| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.92 r_work: 0.3390 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11067 Z= 0.133 Angle : 0.494 6.166 15033 Z= 0.260 Chirality : 0.039 0.153 1750 Planarity : 0.004 0.049 1845 Dihedral : 7.826 76.382 1522 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.78 % Allowed : 18.70 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1333 helix: 1.91 (0.17), residues: 883 sheet: -1.76 (0.91), residues: 28 loop : -0.77 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1291 TYR 0.025 0.001 TYR B1032 PHE 0.023 0.001 PHE B 551 TRP 0.009 0.001 TRP B1197 HIS 0.013 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00304 (11067) covalent geometry : angle 0.49401 (15033) hydrogen bonds : bond 0.03936 ( 699) hydrogen bonds : angle 4.03692 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 262 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7890 (mtpt) REVERT: B 365 PHE cc_start: 0.8511 (t80) cc_final: 0.8304 (t80) REVERT: B 485 MET cc_start: 0.7726 (mmt) cc_final: 0.7045 (mtm) REVERT: B 505 MET cc_start: 0.8086 (mmm) cc_final: 0.7654 (mmm) REVERT: B 626 ASP cc_start: 0.7434 (t0) cc_final: 0.7186 (t0) REVERT: B 679 GLN cc_start: 0.7405 (pm20) cc_final: 0.6906 (mt0) REVERT: B 734 GLU cc_start: 0.8112 (tp30) cc_final: 0.7633 (mp0) REVERT: B 804 LYS cc_start: 0.8337 (tttt) cc_final: 0.8083 (ttmm) REVERT: B 808 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8300 (mm-30) REVERT: B 951 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7606 (mptt) REVERT: B 1085 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (mpp) REVERT: B 1088 GLN cc_start: 0.8229 (tt0) cc_final: 0.7664 (tp-100) REVERT: B 1094 MET cc_start: 0.8424 (mmm) cc_final: 0.8089 (mmm) REVERT: B 1106 ILE cc_start: 0.8586 (mm) cc_final: 0.8373 (mt) REVERT: B 1139 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8027 (mm) REVERT: B 1179 LEU cc_start: 0.8333 (mp) cc_final: 0.7983 (mm) REVERT: B 1264 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7647 (mtpp) REVERT: B 1343 LYS cc_start: 0.8238 (tppt) cc_final: 0.7848 (mmmt) REVERT: B 1414 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 1476 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: B 1523 MET cc_start: 0.8749 (mtp) cc_final: 0.8491 (mtt) outliers start: 33 outliers final: 19 residues processed: 191 average time/residue: 0.1245 time to fit residues: 32.6657 Evaluate side-chains 177 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 966 MET Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1244 ASN Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127369 restraints weight = 12024.914| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.87 r_work: 0.3332 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11067 Z= 0.174 Angle : 0.534 6.412 15033 Z= 0.280 Chirality : 0.041 0.160 1750 Planarity : 0.004 0.051 1845 Dihedral : 7.803 75.441 1522 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.78 % Allowed : 19.12 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1333 helix: 1.79 (0.17), residues: 890 sheet: -1.81 (0.92), residues: 28 loop : -0.81 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1248 TYR 0.025 0.001 TYR B1032 PHE 0.015 0.001 PHE B 589 TRP 0.022 0.001 TRP B1507 HIS 0.013 0.002 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00413 (11067) covalent geometry : angle 0.53423 (15033) hydrogen bonds : bond 0.04126 ( 699) hydrogen bonds : angle 4.08758 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: B 262 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7867 (mtpt) REVERT: B 365 PHE cc_start: 0.8538 (t80) cc_final: 0.8290 (t80) REVERT: B 380 VAL cc_start: 0.8833 (t) cc_final: 0.8541 (m) REVERT: B 505 MET cc_start: 0.8146 (mmm) cc_final: 0.7747 (mmm) REVERT: B 626 ASP cc_start: 0.7482 (t0) cc_final: 0.7218 (t0) REVERT: B 679 GLN cc_start: 0.7437 (pm20) cc_final: 0.6958 (mt0) REVERT: B 734 GLU cc_start: 0.8146 (tp30) cc_final: 0.7697 (mp0) REVERT: B 804 LYS cc_start: 0.8396 (tttt) cc_final: 0.8103 (ttmm) REVERT: B 808 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8268 (mm-30) REVERT: B 951 LYS cc_start: 0.7909 (ttpp) cc_final: 0.7583 (mptt) REVERT: B 1085 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: B 1088 GLN cc_start: 0.8221 (tt0) cc_final: 0.7667 (tp-100) REVERT: B 1094 MET cc_start: 0.8472 (mmm) cc_final: 0.8264 (mmt) REVERT: B 1106 ILE cc_start: 0.8566 (mm) cc_final: 0.8354 (mt) REVERT: B 1139 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 1179 LEU cc_start: 0.8345 (mp) cc_final: 0.7992 (mm) REVERT: B 1264 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7644 (mtpp) REVERT: B 1311 HIS cc_start: 0.7340 (m-70) cc_final: 0.7047 (m90) REVERT: B 1315 THR cc_start: 0.8757 (p) cc_final: 0.8521 (p) REVERT: B 1325 VAL cc_start: 0.8910 (p) cc_final: 0.8585 (m) REVERT: B 1343 LYS cc_start: 0.8203 (tppt) cc_final: 0.7790 (mmmt) REVERT: B 1347 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: B 1414 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7968 (mp) REVERT: B 1523 MET cc_start: 0.8839 (mtp) cc_final: 0.8636 (mtt) outliers start: 33 outliers final: 22 residues processed: 180 average time/residue: 0.1201 time to fit residues: 30.4134 Evaluate side-chains 169 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1267 SER Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1527 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128261 restraints weight = 12090.869| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.92 r_work: 0.3341 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11067 Z= 0.147 Angle : 0.506 6.805 15033 Z= 0.265 Chirality : 0.040 0.173 1750 Planarity : 0.004 0.050 1845 Dihedral : 7.713 76.370 1522 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.86 % Allowed : 19.29 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1333 helix: 1.88 (0.17), residues: 892 sheet: -3.37 (0.75), residues: 34 loop : -0.62 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1291 TYR 0.024 0.001 TYR B1032 PHE 0.015 0.001 PHE B 589 TRP 0.019 0.001 TRP B1507 HIS 0.012 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00343 (11067) covalent geometry : angle 0.50650 (15033) hydrogen bonds : bond 0.03949 ( 699) hydrogen bonds : angle 4.02429 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.7439 (mmm) cc_final: 0.7238 (mmp) REVERT: B 210 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: B 219 ILE cc_start: 0.7923 (mm) cc_final: 0.7576 (pt) REVERT: B 262 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7872 (mtpt) REVERT: B 327 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6719 (ptm) REVERT: B 365 PHE cc_start: 0.8569 (t80) cc_final: 0.8319 (t80) REVERT: B 505 MET cc_start: 0.8138 (mmm) cc_final: 0.7717 (mmm) REVERT: B 626 ASP cc_start: 0.7612 (t0) cc_final: 0.7321 (t0) REVERT: B 679 GLN cc_start: 0.7376 (pm20) cc_final: 0.6991 (mt0) REVERT: B 734 GLU cc_start: 0.8110 (tp30) cc_final: 0.7727 (mp0) REVERT: B 804 LYS cc_start: 0.8420 (tttt) cc_final: 0.8113 (ttmm) REVERT: B 808 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8229 (mm-30) REVERT: B 951 LYS cc_start: 0.7900 (ttpp) cc_final: 0.7591 (mptt) REVERT: B 1085 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (mpp) REVERT: B 1088 GLN cc_start: 0.8192 (tt0) cc_final: 0.7670 (tp-100) REVERT: B 1094 MET cc_start: 0.8475 (mmm) cc_final: 0.8256 (mmt) REVERT: B 1106 ILE cc_start: 0.8592 (mm) cc_final: 0.8380 (mt) REVERT: B 1139 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8046 (mm) REVERT: B 1179 LEU cc_start: 0.8324 (mp) cc_final: 0.7972 (mm) REVERT: B 1211 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7636 (tp) REVERT: B 1248 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7802 (mtm-85) REVERT: B 1264 LYS cc_start: 0.8080 (mmtt) cc_final: 0.7654 (mtpp) REVERT: B 1311 HIS cc_start: 0.7235 (m-70) cc_final: 0.6926 (m90) REVERT: B 1325 VAL cc_start: 0.8873 (p) cc_final: 0.8608 (m) REVERT: B 1343 LYS cc_start: 0.8133 (tppt) cc_final: 0.7817 (mmmt) REVERT: B 1347 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6508 (pp20) REVERT: B 1414 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 1476 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: B 1523 MET cc_start: 0.8824 (mtp) cc_final: 0.8621 (mtt) outliers start: 34 outliers final: 20 residues processed: 177 average time/residue: 0.1137 time to fit residues: 27.7046 Evaluate side-chains 172 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127611 restraints weight = 12003.905| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.95 r_work: 0.3344 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11067 Z= 0.150 Angle : 0.512 6.380 15033 Z= 0.268 Chirality : 0.040 0.157 1750 Planarity : 0.004 0.050 1845 Dihedral : 7.633 78.690 1522 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.03 % Allowed : 19.21 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1333 helix: 1.91 (0.17), residues: 891 sheet: -3.06 (0.79), residues: 37 loop : -0.58 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1291 TYR 0.023 0.001 TYR B1032 PHE 0.015 0.001 PHE B 589 TRP 0.009 0.001 TRP B 994 HIS 0.012 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00351 (11067) covalent geometry : angle 0.51234 (15033) hydrogen bonds : bond 0.03945 ( 699) hydrogen bonds : angle 4.01568 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: B 138 MET cc_start: 0.7481 (mmm) cc_final: 0.7246 (mmp) REVERT: B 210 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: B 219 ILE cc_start: 0.7927 (mm) cc_final: 0.7570 (pt) REVERT: B 262 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7871 (mtpt) REVERT: B 327 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6783 (ptm) REVERT: B 365 PHE cc_start: 0.8610 (t80) cc_final: 0.8308 (t80) REVERT: B 485 MET cc_start: 0.7980 (mmt) cc_final: 0.7354 (ptm) REVERT: B 498 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8772 (mtpp) REVERT: B 505 MET cc_start: 0.8162 (mmm) cc_final: 0.7734 (mmm) REVERT: B 522 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8469 (mm) REVERT: B 626 ASP cc_start: 0.7628 (t0) cc_final: 0.7307 (t0) REVERT: B 679 GLN cc_start: 0.7427 (pm20) cc_final: 0.7116 (mt0) REVERT: B 734 GLU cc_start: 0.8106 (tp30) cc_final: 0.7698 (mp0) REVERT: B 804 LYS cc_start: 0.8414 (tttt) cc_final: 0.8107 (ttmm) REVERT: B 808 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8205 (mm-30) REVERT: B 951 LYS cc_start: 0.7967 (ttpp) cc_final: 0.7573 (mptt) REVERT: B 1085 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: B 1088 GLN cc_start: 0.8314 (tt0) cc_final: 0.7696 (tp-100) REVERT: B 1106 ILE cc_start: 0.8597 (mm) cc_final: 0.8379 (mt) REVERT: B 1139 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8160 (mm) REVERT: B 1179 LEU cc_start: 0.8362 (mp) cc_final: 0.8018 (mm) REVERT: B 1248 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: B 1264 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7661 (mtpp) REVERT: B 1315 THR cc_start: 0.8803 (p) cc_final: 0.8567 (p) REVERT: B 1325 VAL cc_start: 0.8885 (p) cc_final: 0.8626 (m) REVERT: B 1343 LYS cc_start: 0.8136 (tppt) cc_final: 0.7802 (mmmt) REVERT: B 1347 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6571 (pp20) REVERT: B 1414 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7909 (mp) REVERT: B 1476 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: B 1515 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7241 (mt0) outliers start: 36 outliers final: 22 residues processed: 185 average time/residue: 0.1048 time to fit residues: 27.0957 Evaluate side-chains 177 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 131 optimal weight: 0.3980 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127801 restraints weight = 12053.414| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.79 r_work: 0.3329 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11067 Z= 0.149 Angle : 0.509 6.427 15033 Z= 0.267 Chirality : 0.040 0.158 1750 Planarity : 0.004 0.051 1845 Dihedral : 7.603 79.902 1522 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.12 % Allowed : 19.12 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.23), residues: 1333 helix: 1.91 (0.17), residues: 893 sheet: -3.05 (0.80), residues: 37 loop : -0.59 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1291 TYR 0.023 0.001 TYR B1032 PHE 0.015 0.001 PHE B 589 TRP 0.009 0.001 TRP B 994 HIS 0.011 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00349 (11067) covalent geometry : angle 0.50916 (15033) hydrogen bonds : bond 0.03935 ( 699) hydrogen bonds : angle 3.99596 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 210 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: B 219 ILE cc_start: 0.7948 (mm) cc_final: 0.7616 (pt) REVERT: B 262 LYS cc_start: 0.8192 (ttmm) cc_final: 0.7888 (mtpt) REVERT: B 327 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6783 (ptm) REVERT: B 365 PHE cc_start: 0.8635 (t80) cc_final: 0.8359 (t80) REVERT: B 485 MET cc_start: 0.7959 (mmt) cc_final: 0.7357 (ptm) REVERT: B 505 MET cc_start: 0.8178 (mmm) cc_final: 0.7739 (mmm) REVERT: B 522 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8482 (mm) REVERT: B 626 ASP cc_start: 0.7644 (t0) cc_final: 0.7309 (t0) REVERT: B 679 GLN cc_start: 0.7425 (pm20) cc_final: 0.7116 (mt0) REVERT: B 734 GLU cc_start: 0.8004 (tp30) cc_final: 0.7643 (mp0) REVERT: B 804 LYS cc_start: 0.8419 (tttt) cc_final: 0.8109 (ttmm) REVERT: B 808 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8188 (mm-30) REVERT: B 951 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7567 (mptt) REVERT: B 1034 MET cc_start: 0.7585 (mmm) cc_final: 0.7206 (tpt) REVERT: B 1065 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7321 (ptp90) REVERT: B 1085 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7828 (mpp) REVERT: B 1088 GLN cc_start: 0.8322 (tt0) cc_final: 0.7719 (tp-100) REVERT: B 1139 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8035 (mm) REVERT: B 1179 LEU cc_start: 0.8370 (mp) cc_final: 0.8028 (mm) REVERT: B 1211 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7579 (tp) REVERT: B 1234 SER cc_start: 0.8590 (t) cc_final: 0.8182 (p) REVERT: B 1248 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: B 1264 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7668 (mtpp) REVERT: B 1315 THR cc_start: 0.8793 (p) cc_final: 0.8543 (p) REVERT: B 1325 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8649 (m) REVERT: B 1343 LYS cc_start: 0.8148 (tppt) cc_final: 0.7809 (mmmt) REVERT: B 1347 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6544 (pp20) REVERT: B 1414 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 1476 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: B 1515 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7261 (mt0) outliers start: 37 outliers final: 25 residues processed: 181 average time/residue: 0.1205 time to fit residues: 30.2924 Evaluate side-chains 184 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1322 VAL Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1465 ASP Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 116 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127155 restraints weight = 12025.421| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.04 r_work: 0.3334 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11067 Z= 0.142 Angle : 0.505 6.457 15033 Z= 0.264 Chirality : 0.040 0.163 1750 Planarity : 0.004 0.051 1845 Dihedral : 7.555 81.151 1522 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.03 % Allowed : 19.21 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1333 helix: 1.96 (0.17), residues: 893 sheet: -3.11 (0.78), residues: 37 loop : -0.56 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1291 TYR 0.023 0.001 TYR B1032 PHE 0.014 0.001 PHE B 589 TRP 0.010 0.001 TRP B 994 HIS 0.011 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00331 (11067) covalent geometry : angle 0.50497 (15033) hydrogen bonds : bond 0.03883 ( 699) hydrogen bonds : angle 3.99030 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 210 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: B 219 ILE cc_start: 0.7942 (mm) cc_final: 0.7615 (pt) REVERT: B 262 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7875 (mtpt) REVERT: B 327 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6844 (ptm) REVERT: B 365 PHE cc_start: 0.8642 (t80) cc_final: 0.8356 (t80) REVERT: B 485 MET cc_start: 0.7959 (mmt) cc_final: 0.7344 (ptm) REVERT: B 505 MET cc_start: 0.8177 (mmm) cc_final: 0.7733 (mmm) REVERT: B 626 ASP cc_start: 0.7644 (t0) cc_final: 0.7298 (t0) REVERT: B 679 GLN cc_start: 0.7423 (pm20) cc_final: 0.7098 (mt0) REVERT: B 734 GLU cc_start: 0.8050 (tp30) cc_final: 0.7636 (mp0) REVERT: B 804 LYS cc_start: 0.8403 (tttt) cc_final: 0.8097 (ttmm) REVERT: B 808 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8151 (mm-30) REVERT: B 951 LYS cc_start: 0.7923 (ttpp) cc_final: 0.7535 (mptt) REVERT: B 1065 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: B 1085 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7854 (mpp) REVERT: B 1088 GLN cc_start: 0.8304 (tt0) cc_final: 0.7688 (tp-100) REVERT: B 1139 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8068 (mm) REVERT: B 1179 LEU cc_start: 0.8381 (mp) cc_final: 0.8039 (mm) REVERT: B 1211 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7585 (tp) REVERT: B 1234 SER cc_start: 0.8596 (t) cc_final: 0.8180 (p) REVERT: B 1248 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7713 (mtm-85) REVERT: B 1264 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7647 (mtpp) REVERT: B 1315 THR cc_start: 0.8818 (p) cc_final: 0.8580 (p) REVERT: B 1325 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8696 (m) REVERT: B 1343 LYS cc_start: 0.8090 (tppt) cc_final: 0.7799 (mmmt) REVERT: B 1347 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: B 1355 ILE cc_start: 0.7899 (mt) cc_final: 0.7590 (mt) REVERT: B 1414 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 1476 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7215 (m-30) REVERT: B 1515 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7287 (mt0) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.1029 time to fit residues: 25.5733 Evaluate side-chains 185 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1322 VAL Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1465 ASP Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 0.0060 chunk 109 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127238 restraints weight = 12062.578| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.80 r_work: 0.3334 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11067 Z= 0.151 Angle : 0.515 7.107 15033 Z= 0.269 Chirality : 0.040 0.180 1750 Planarity : 0.004 0.051 1845 Dihedral : 7.545 81.586 1522 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.20 % Allowed : 19.04 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.23), residues: 1333 helix: 1.95 (0.17), residues: 893 sheet: -3.09 (0.78), residues: 37 loop : -0.57 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1291 TYR 0.023 0.001 TYR B1032 PHE 0.014 0.001 PHE B 589 TRP 0.009 0.001 TRP B 994 HIS 0.014 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00354 (11067) covalent geometry : angle 0.51523 (15033) hydrogen bonds : bond 0.03913 ( 699) hydrogen bonds : angle 4.00180 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 210 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 219 ILE cc_start: 0.7950 (mm) cc_final: 0.7611 (pt) REVERT: B 262 LYS cc_start: 0.8182 (ttmm) cc_final: 0.7881 (mtpt) REVERT: B 327 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6841 (ptm) REVERT: B 365 PHE cc_start: 0.8639 (t80) cc_final: 0.8316 (t80) REVERT: B 475 LEU cc_start: 0.8631 (tt) cc_final: 0.8285 (tp) REVERT: B 485 MET cc_start: 0.7923 (mmt) cc_final: 0.7340 (ptm) REVERT: B 505 MET cc_start: 0.8173 (mmm) cc_final: 0.7728 (mmm) REVERT: B 522 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8483 (mm) REVERT: B 626 ASP cc_start: 0.7649 (t0) cc_final: 0.7297 (t0) REVERT: B 679 GLN cc_start: 0.7479 (pm20) cc_final: 0.7176 (mt0) REVERT: B 734 GLU cc_start: 0.7989 (tp30) cc_final: 0.7608 (mp0) REVERT: B 804 LYS cc_start: 0.8392 (tttt) cc_final: 0.8078 (ttmm) REVERT: B 808 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8131 (mm-30) REVERT: B 951 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7534 (mptt) REVERT: B 1034 MET cc_start: 0.7575 (mmm) cc_final: 0.7209 (tpt) REVERT: B 1065 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7332 (ptp90) REVERT: B 1085 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7843 (mpp) REVERT: B 1088 GLN cc_start: 0.8289 (tt0) cc_final: 0.7677 (tp-100) REVERT: B 1139 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 1179 LEU cc_start: 0.8399 (mp) cc_final: 0.8057 (mm) REVERT: B 1211 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7565 (tp) REVERT: B 1234 SER cc_start: 0.8611 (t) cc_final: 0.8213 (p) REVERT: B 1248 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7691 (mtm-85) REVERT: B 1264 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7657 (mtpp) REVERT: B 1315 THR cc_start: 0.8850 (p) cc_final: 0.8600 (p) REVERT: B 1325 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 1343 LYS cc_start: 0.8087 (tppt) cc_final: 0.7797 (mmmt) REVERT: B 1347 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6619 (pp20) REVERT: B 1355 ILE cc_start: 0.7900 (mt) cc_final: 0.7595 (mt) REVERT: B 1414 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7895 (mp) REVERT: B 1476 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: B 1515 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7290 (mt0) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.1186 time to fit residues: 30.0942 Evaluate side-chains 185 residues out of total 1187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 318 TYR Chi-restraints excluded: chain B residue 327 MET Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 604 SER Chi-restraints excluded: chain B residue 622 HIS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1085 MET Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1211 LEU Chi-restraints excluded: chain B residue 1257 ILE Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1314 VAL Chi-restraints excluded: chain B residue 1322 VAL Chi-restraints excluded: chain B residue 1325 VAL Chi-restraints excluded: chain B residue 1328 THR Chi-restraints excluded: chain B residue 1347 GLU Chi-restraints excluded: chain B residue 1382 SER Chi-restraints excluded: chain B residue 1414 LEU Chi-restraints excluded: chain B residue 1465 ASP Chi-restraints excluded: chain B residue 1476 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.163116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126871 restraints weight = 12114.064| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.03 r_work: 0.3331 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11067 Z= 0.147 Angle : 0.512 6.952 15033 Z= 0.267 Chirality : 0.040 0.175 1750 Planarity : 0.004 0.051 1845 Dihedral : 7.525 82.394 1522 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.29 % Allowed : 19.04 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.23), residues: 1333 helix: 2.00 (0.17), residues: 891 sheet: -3.09 (0.77), residues: 37 loop : -0.60 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1291 TYR 0.023 0.001 TYR B1032 PHE 0.014 0.001 PHE B 589 TRP 0.009 0.001 TRP B 994 HIS 0.013 0.001 HIS B 382 Details of bonding type rmsd covalent geometry : bond 0.00343 (11067) covalent geometry : angle 0.51214 (15033) hydrogen bonds : bond 0.03888 ( 699) hydrogen bonds : angle 3.99302 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.93 seconds wall clock time: 50 minutes 0.97 seconds (3000.97 seconds total)