Starting phenix.real_space_refine on Mon May 4 10:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746.map" model { file = "/net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ztc_74746/05_2026/9ztc_74746_trim.cif" } resolution = 3.5 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 6656 2.51 5 N 1723 2.21 5 O 1747 1.98 5 H 9140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19316 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 19207 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1290} Chain breaks: 14 Unresolved non-hydrogen bonds: 972 Unresolved non-hydrogen angles: 1226 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'GLU:plan': 37, 'ASP:plan': 18, 'ASN:plan1': 9, 'GLN:plan1': 10, 'ARG:plan': 22, 'HIS:plan': 5, 'TYR:plan': 7, 'TRP:plan': 4, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 531 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.65, per 1000 atoms: 0.19 Number of scatterers: 19316 At special positions: 0 Unit cell: (90.2, 113.16, 132.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1747 8.00 N 1723 7.00 C 6656 6.00 H 9140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1345 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A1849 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 597.6 milliseconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 2 sheets defined 71.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 148 through 154 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.721A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.675A pdb=" N LYS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.574A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASN A 280 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 338 Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.601A pdb=" N GLN A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 357 through 369 removed outlier: 4.186A pdb=" N ILE A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.520A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.576A pdb=" N LYS A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.520A pdb=" N ARG A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 423' Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.668A pdb=" N VAL A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.682A pdb=" N HIS A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'A' and resid 488 through 518 removed outlier: 3.855A pdb=" N GLY A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 552 removed outlier: 3.858A pdb=" N LEU A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 559 through 583 Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.068A pdb=" N MET A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 594' Processing helix chain 'A' and resid 615 through 640 removed outlier: 3.960A pdb=" N TRP A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.796A pdb=" N VAL A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 713 removed outlier: 3.836A pdb=" N THR A 692 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.790A pdb=" N HIS A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 935 through 947 Processing helix chain 'A' and resid 949 through 972 removed outlier: 4.449A pdb=" N TYR A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 980 removed outlier: 3.552A pdb=" N VAL A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1011 through 1025 Processing helix chain 'A' and resid 1081 through 1091 removed outlier: 4.470A pdb=" N ASN A1085 " --> pdb=" O GLY A1081 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A1091 " --> pdb=" O ASN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1121 removed outlier: 4.847A pdb=" N ARG A1116 " --> pdb=" O CYS A1112 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 4.065A pdb=" N SER A1185 " --> pdb=" O ALA A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1205 Processing helix chain 'A' and resid 1206 through 1208 No H-bonds generated for 'chain 'A' and resid 1206 through 1208' Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.888A pdb=" N GLY A1226 " --> pdb=" O ASP A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1272 Processing helix chain 'A' and resid 1272 through 1282 Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1294 through 1325 removed outlier: 4.410A pdb=" N HIS A1298 " --> pdb=" O HIS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1382 removed outlier: 3.509A pdb=" N TRP A1354 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A1355 " --> pdb=" O ALA A1351 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG A1356 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Proline residue: A1372 - end of helix Processing helix chain 'A' and resid 1382 through 1392 Processing helix chain 'A' and resid 1437 through 1447 removed outlier: 4.489A pdb=" N GLY A1447 " --> pdb=" O SER A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1448 through 1467 removed outlier: 3.894A pdb=" N MET A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1490 removed outlier: 3.838A pdb=" N PHE A1475 " --> pdb=" O PRO A1471 " (cutoff:3.500A) Proline residue: A1486 - end of helix Processing helix chain 'A' and resid 1495 through 1512 Processing helix chain 'A' and resid 1521 through 1529 Processing helix chain 'A' and resid 1558 through 1583 Proline residue: A1567 - end of helix Processing helix chain 'A' and resid 1598 through 1621 Proline residue: A1609 - end of helix Processing helix chain 'A' and resid 1640 through 1665 Processing helix chain 'A' and resid 1668 through 1695 removed outlier: 3.541A pdb=" N ILE A1674 " --> pdb=" O VAL A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1754 Processing helix chain 'A' and resid 1754 through 1760 Processing helix chain 'A' and resid 1762 through 1775 Processing helix chain 'A' and resid 1786 through 1825 removed outlier: 3.576A pdb=" N SER A1802 " --> pdb=" O LYS A1798 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A1803 " --> pdb=" O LYS A1799 " (cutoff:3.500A) Proline residue: A1818 - end of helix removed outlier: 3.869A pdb=" N ALA A1823 " --> pdb=" O ALA A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1838 Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 1068 through 1071 removed outlier: 3.794A pdb=" N PHE A1068 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A1033 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 842 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A1001 " --> pdb=" O PHE A 842 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL A 844 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER A1003 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR A 846 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 843 " --> pdb=" O GLN A1099 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1100 " --> pdb=" O ASP A1197 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A1197 " --> pdb=" O LEU A1100 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A1149 " --> pdb=" O ASN A1200 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ARG A1235 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR A1241 " --> pdb=" O ARG A1154 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1989 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: 4.51 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9127 1.03 - 1.23: 22 1.23 - 1.42: 4520 1.42 - 1.61: 5839 1.61 - 1.81: 83 Bond restraints: 19591 Sorted by residual: bond pdb=" CAY Y01 A2001 " pdb=" OAW Y01 A2001 " ideal model delta sigma weight residual 1.332 1.435 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" CAY Y01 A2002 " pdb=" OAW Y01 A2002 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ILE A1784 " pdb=" CA ILE A1784 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.55e+00 bond pdb=" C TRP A 445 " pdb=" O TRP A 445 " ideal model delta sigma weight residual 1.236 1.203 0.034 1.18e-02 7.18e+03 8.22e+00 bond pdb=" C THR A 444 " pdb=" O THR A 444 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.17e-02 7.31e+03 7.46e+00 ... (remaining 19586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.92: 35019 5.92 - 11.84: 10 11.84 - 17.76: 2 17.76 - 23.68: 4 23.68 - 29.60: 8 Bond angle restraints: 35043 Sorted by residual: angle pdb=" CG1 ILE A1368 " pdb=" CD1 ILE A1368 " pdb="HD12 ILE A1368 " ideal model delta sigma weight residual 109.00 79.40 29.60 3.00e+00 1.11e-01 9.74e+01 angle pdb=" CG1 ILE A1362 " pdb=" CD1 ILE A1362 " pdb="HD11 ILE A1362 " ideal model delta sigma weight residual 109.00 79.44 29.56 3.00e+00 1.11e-01 9.71e+01 angle pdb=" CG1 ILE A1368 " pdb=" CD1 ILE A1368 " pdb="HD13 ILE A1368 " ideal model delta sigma weight residual 109.00 79.59 29.41 3.00e+00 1.11e-01 9.61e+01 angle pdb=" CG1 ILE A1362 " pdb=" CD1 ILE A1362 " pdb="HD12 ILE A1362 " ideal model delta sigma weight residual 109.00 79.66 29.34 3.00e+00 1.11e-01 9.56e+01 angle pdb="HD11 ILE A1368 " pdb=" CD1 ILE A1368 " pdb="HD12 ILE A1368 " ideal model delta sigma weight residual 110.00 81.08 28.92 3.00e+00 1.11e-01 9.29e+01 ... (remaining 35038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.67: 9137 21.67 - 43.33: 353 43.33 - 65.00: 119 65.00 - 86.66: 12 86.66 - 108.33: 5 Dihedral angle restraints: 9626 sinusoidal: 4780 harmonic: 4846 Sorted by residual: dihedral pdb=" CA PHE A 957 " pdb=" C PHE A 957 " pdb=" N MET A 958 " pdb=" CA MET A 958 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.62 108.33 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.59 106.21 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 9623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1510 0.080 - 0.159: 98 0.159 - 0.239: 2 0.239 - 0.318: 5 0.318 - 0.398: 5 Chirality restraints: 1620 Sorted by residual: chirality pdb=" CBH Y01 A2001 " pdb=" CAT Y01 A2001 " pdb=" CAZ Y01 A2001 " pdb=" CBF Y01 A2001 " both_signs ideal model delta sigma weight residual False -2.85 -3.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBF Y01 A2001 " pdb=" CAS Y01 A2001 " pdb=" CBD Y01 A2001 " pdb=" CBH Y01 A2001 " both_signs ideal model delta sigma weight residual False -2.45 -2.83 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CBH Y01 A2002 " pdb=" CAT Y01 A2002 " pdb=" CAZ Y01 A2002 " pdb=" CBF Y01 A2002 " both_signs ideal model delta sigma weight residual False -2.85 -3.23 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 1617 not shown) Planarity restraints: 3079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1783 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C PRO A1783 " -0.041 2.00e-02 2.50e+03 pdb=" O PRO A1783 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A1784 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 642 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 643 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1790 " 0.007 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" N ARG A1791 " -0.022 2.00e-02 2.50e+03 pdb=" CA ARG A1791 " 0.006 2.00e-02 2.50e+03 pdb=" H ARG A1791 " 0.009 2.00e-02 2.50e+03 ... (remaining 3076 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 982 2.21 - 2.81: 38551 2.81 - 3.40: 53799 3.40 - 4.00: 67652 4.00 - 4.60: 105208 Nonbonded interactions: 266192 Sorted by model distance: nonbonded pdb=" O THR A 218 " pdb="HH22 ARG A1207 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU A1221 " pdb=" H GLU A1221 " model vdw 1.635 2.450 nonbonded pdb=" OD1 ASP A 392 " pdb="HH22 ARG A1273 " model vdw 1.648 2.450 nonbonded pdb=" O LEU A 354 " pdb=" HG1 THR A 359 " model vdw 1.668 2.450 nonbonded pdb=" OG1 THR A 659 " pdb=" HG1 THR A1590 " model vdw 1.670 2.450 ... (remaining 266187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 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: 0.130 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.960 Find NCS groups from input model: 0.080 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.003 0.103 10456 Z= 0.185 Angle : 0.595 12.702 14286 Z= 0.306 Chirality : 0.046 0.398 1620 Planarity : 0.004 0.043 1807 Dihedral : 12.357 108.327 3621 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.44 % Allowed : 4.08 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.23), residues: 1320 helix: 2.60 (0.17), residues: 846 sheet: -0.01 (0.59), residues: 52 loop : 0.03 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1069 TYR 0.009 0.001 TYR A1048 PHE 0.014 0.001 PHE A 685 TRP 0.008 0.001 TRP A 289 HIS 0.005 0.001 HIS A1654 Details of bonding type rmsd covalent geometry : bond 0.00341 (10451) covalent geometry : angle 0.59396 (14273) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.33655 ( 4) hydrogen bonds : bond 0.15413 ( 673) hydrogen bonds : angle 5.42375 ( 1989) link_BETA1-4 : bond 0.00539 ( 2) link_BETA1-4 : angle 1.52485 ( 6) link_NAG-ASN : bond 0.00413 ( 1) link_NAG-ASN : angle 1.50369 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8747 (t0) cc_final: 0.8489 (t70) REVERT: A 293 MET cc_start: 0.8219 (mmt) cc_final: 0.7988 (mmt) REVERT: A 394 ASN cc_start: 0.7968 (t0) cc_final: 0.7479 (t0) REVERT: A 467 PHE cc_start: 0.8617 (m-80) cc_final: 0.8372 (m-80) REVERT: A 534 PHE cc_start: 0.8393 (m-80) cc_final: 0.8083 (m-10) REVERT: A 978 MET cc_start: 0.8661 (tmt) cc_final: 0.8382 (tmm) REVERT: A 1108 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6929 (m-10) REVERT: A 1310 MET cc_start: 0.8905 (mmm) cc_final: 0.8402 (mmm) REVERT: A 1652 ILE cc_start: 0.9278 (tt) cc_final: 0.9076 (tp) REVERT: A 1672 MET cc_start: 0.8814 (tmm) cc_final: 0.8574 (tmm) outliers start: 4 outliers final: 2 residues processed: 238 average time/residue: 0.2104 time to fit residues: 71.3262 Evaluate side-chains 156 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1108 TYR Chi-restraints excluded: chain A residue 1571 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092678 restraints weight = 67635.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.096456 restraints weight = 24388.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.098981 restraints weight = 13156.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100469 restraints weight = 8822.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101468 restraints weight = 6841.692| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10456 Z= 0.173 Angle : 0.539 5.320 14286 Z= 0.290 Chirality : 0.038 0.162 1620 Planarity : 0.004 0.066 1807 Dihedral : 6.891 61.625 1661 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.10 % Allowed : 10.26 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.23), residues: 1320 helix: 2.30 (0.17), residues: 866 sheet: -0.77 (0.59), residues: 60 loop : 0.17 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1065 TYR 0.013 0.001 TYR A1292 PHE 0.016 0.001 PHE A 685 TRP 0.009 0.001 TRP A1354 HIS 0.004 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00359 (10451) covalent geometry : angle 0.53627 (14273) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.54350 ( 4) hydrogen bonds : bond 0.05511 ( 673) hydrogen bonds : angle 4.79676 ( 1989) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 2.45606 ( 6) link_NAG-ASN : bond 0.00339 ( 1) link_NAG-ASN : angle 0.78914 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8745 (t0) cc_final: 0.8454 (t70) REVERT: A 394 ASN cc_start: 0.8103 (t0) cc_final: 0.7558 (t0) REVERT: A 458 MET cc_start: 0.8035 (mtt) cc_final: 0.7814 (ttt) REVERT: A 470 ASN cc_start: 0.8345 (t0) cc_final: 0.8027 (t0) REVERT: A 534 PHE cc_start: 0.8496 (m-80) cc_final: 0.8136 (m-10) REVERT: A 541 ILE cc_start: 0.9165 (tp) cc_final: 0.8862 (tp) REVERT: A 978 MET cc_start: 0.8597 (tmt) cc_final: 0.8329 (tmm) REVERT: A 1672 MET cc_start: 0.8877 (tmm) cc_final: 0.8640 (tmm) outliers start: 10 outliers final: 9 residues processed: 165 average time/residue: 0.1709 time to fit residues: 42.7261 Evaluate side-chains 149 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 522 TRP Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1655 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 44 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 GLN A1269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091364 restraints weight = 68182.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095069 restraints weight = 25157.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097505 restraints weight = 13775.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098751 restraints weight = 9387.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099870 restraints weight = 7551.477| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10456 Z= 0.202 Angle : 0.532 5.295 14286 Z= 0.288 Chirality : 0.038 0.173 1620 Planarity : 0.004 0.032 1807 Dihedral : 5.837 58.847 1657 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.10 % Allowed : 10.26 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.23), residues: 1320 helix: 2.25 (0.17), residues: 868 sheet: -0.94 (0.64), residues: 60 loop : 0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1601 TYR 0.015 0.001 TYR A 633 PHE 0.011 0.001 PHE A 685 TRP 0.008 0.001 TRP A1354 HIS 0.004 0.001 HIS A1654 Details of bonding type rmsd covalent geometry : bond 0.00431 (10451) covalent geometry : angle 0.53006 (14273) SS BOND : bond 0.00327 ( 2) SS BOND : angle 0.31617 ( 4) hydrogen bonds : bond 0.05262 ( 673) hydrogen bonds : angle 4.67662 ( 1989) link_BETA1-4 : bond 0.00325 ( 2) link_BETA1-4 : angle 2.40821 ( 6) link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 0.99590 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8658 (t0) cc_final: 0.8370 (t70) REVERT: A 394 ASN cc_start: 0.8314 (t0) cc_final: 0.7821 (t0) REVERT: A 534 PHE cc_start: 0.8479 (m-80) cc_final: 0.8151 (m-10) REVERT: A 541 ILE cc_start: 0.9212 (tp) cc_final: 0.8924 (tp) REVERT: A 978 MET cc_start: 0.8505 (tmt) cc_final: 0.8244 (tmm) REVERT: A 1672 MET cc_start: 0.8847 (tmm) cc_final: 0.8602 (tmm) outliers start: 19 outliers final: 14 residues processed: 148 average time/residue: 0.1663 time to fit residues: 38.2734 Evaluate side-chains 145 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 522 TRP Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1749 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.111178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092839 restraints weight = 67769.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.096619 restraints weight = 24867.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099086 restraints weight = 13426.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100658 restraints weight = 9045.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.101251 restraints weight = 6983.691| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10456 Z= 0.127 Angle : 0.482 5.014 14286 Z= 0.256 Chirality : 0.037 0.175 1620 Planarity : 0.003 0.034 1807 Dihedral : 5.194 56.966 1657 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.66 % Allowed : 10.26 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.23), residues: 1320 helix: 2.39 (0.17), residues: 868 sheet: -0.85 (0.67), residues: 60 loop : 0.13 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1065 TYR 0.011 0.001 TYR A1292 PHE 0.018 0.001 PHE A 629 TRP 0.007 0.001 TRP A1354 HIS 0.003 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00263 (10451) covalent geometry : angle 0.48016 (14273) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.09700 ( 4) hydrogen bonds : bond 0.04715 ( 673) hydrogen bonds : angle 4.35688 ( 1989) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 1.97466 ( 6) link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 0.90546 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8585 (t0) cc_final: 0.8266 (t70) REVERT: A 534 PHE cc_start: 0.8468 (m-80) cc_final: 0.8137 (m-10) REVERT: A 541 ILE cc_start: 0.9125 (tp) cc_final: 0.8874 (tp) REVERT: A 542 ASN cc_start: 0.9147 (t0) cc_final: 0.8282 (t0) REVERT: A 978 MET cc_start: 0.8479 (tmt) cc_final: 0.8231 (tmm) REVERT: A 1672 MET cc_start: 0.8844 (tmm) cc_final: 0.8601 (tmm) outliers start: 15 outliers final: 14 residues processed: 156 average time/residue: 0.1647 time to fit residues: 40.1100 Evaluate side-chains 150 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1748 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 3.9990 chunk 99 optimal weight: 0.0000 chunk 128 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092569 restraints weight = 67369.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096258 restraints weight = 24430.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098677 restraints weight = 13199.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099934 restraints weight = 8895.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100803 restraints weight = 7106.279| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10456 Z= 0.115 Angle : 0.464 4.987 14286 Z= 0.245 Chirality : 0.036 0.167 1620 Planarity : 0.003 0.033 1807 Dihedral : 4.863 56.329 1657 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.77 % Allowed : 11.15 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.23), residues: 1320 helix: 2.57 (0.17), residues: 870 sheet: -0.82 (0.67), residues: 60 loop : 0.11 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1065 TYR 0.011 0.001 TYR A1292 PHE 0.017 0.001 PHE A1494 TRP 0.007 0.001 TRP A1354 HIS 0.003 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00234 (10451) covalent geometry : angle 0.46326 (14273) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.13210 ( 4) hydrogen bonds : bond 0.04415 ( 673) hydrogen bonds : angle 4.18365 ( 1989) link_BETA1-4 : bond 0.00273 ( 2) link_BETA1-4 : angle 1.62487 ( 6) link_NAG-ASN : bond 0.00204 ( 1) link_NAG-ASN : angle 0.78315 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8567 (t0) cc_final: 0.8268 (t70) REVERT: A 534 PHE cc_start: 0.8468 (m-80) cc_final: 0.8133 (m-10) REVERT: A 541 ILE cc_start: 0.9138 (tp) cc_final: 0.8910 (tp) REVERT: A 542 ASN cc_start: 0.9222 (t0) cc_final: 0.8434 (t0) REVERT: A 978 MET cc_start: 0.8493 (tmt) cc_final: 0.8226 (tmm) REVERT: A 1672 MET cc_start: 0.8797 (tmm) cc_final: 0.8548 (tmm) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.1591 time to fit residues: 38.8516 Evaluate side-chains 151 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1748 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 57 optimal weight: 0.0010 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** A 470 ASN ** 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 = 0.3680 r_free = 0.3680 target = 0.110696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092966 restraints weight = 67614.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096661 restraints weight = 24474.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099031 restraints weight = 13173.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100391 restraints weight = 8905.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.101389 restraints weight = 7020.220| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10456 Z= 0.105 Angle : 0.457 4.897 14286 Z= 0.240 Chirality : 0.036 0.175 1620 Planarity : 0.003 0.034 1807 Dihedral : 4.675 56.138 1657 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.43 % Allowed : 12.14 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.23), residues: 1320 helix: 2.71 (0.17), residues: 864 sheet: -0.80 (0.68), residues: 60 loop : 0.17 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1232 TYR 0.010 0.001 TYR A1292 PHE 0.018 0.001 PHE A 685 TRP 0.006 0.001 TRP A 625 HIS 0.003 0.001 HIS A1748 Details of bonding type rmsd covalent geometry : bond 0.00215 (10451) covalent geometry : angle 0.45619 (14273) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.08869 ( 4) hydrogen bonds : bond 0.04265 ( 673) hydrogen bonds : angle 4.06655 ( 1989) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.48908 ( 6) link_NAG-ASN : bond 0.00277 ( 1) link_NAG-ASN : angle 0.88449 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8530 (t0) cc_final: 0.8239 (t70) REVERT: A 530 ARG cc_start: 0.6654 (mmt180) cc_final: 0.6438 (mmt180) REVERT: A 534 PHE cc_start: 0.8461 (m-80) cc_final: 0.8136 (m-10) REVERT: A 542 ASN cc_start: 0.9219 (t0) cc_final: 0.8465 (t0) REVERT: A 978 MET cc_start: 0.8442 (tmt) cc_final: 0.8160 (tmm) REVERT: A 1672 MET cc_start: 0.8790 (tmm) cc_final: 0.8552 (tmm) outliers start: 13 outliers final: 10 residues processed: 154 average time/residue: 0.1582 time to fit residues: 38.5992 Evaluate side-chains 149 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1748 HIS Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 99 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089446 restraints weight = 69078.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092988 restraints weight = 25463.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095305 restraints weight = 13825.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096480 restraints weight = 9359.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.097337 restraints weight = 7518.662| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 10456 Z= 0.330 Angle : 0.593 5.752 14286 Z= 0.331 Chirality : 0.040 0.192 1620 Planarity : 0.004 0.034 1807 Dihedral : 5.097 54.255 1657 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.10 % Allowed : 12.03 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.23), residues: 1320 helix: 2.23 (0.17), residues: 867 sheet: -1.16 (0.69), residues: 53 loop : -0.20 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 301 TYR 0.015 0.002 TYR A1292 PHE 0.016 0.002 PHE A1475 TRP 0.011 0.001 TRP A 398 HIS 0.007 0.002 HIS A1838 Details of bonding type rmsd covalent geometry : bond 0.00711 (10451) covalent geometry : angle 0.59189 (14273) SS BOND : bond 0.00646 ( 2) SS BOND : angle 0.89743 ( 4) hydrogen bonds : bond 0.05022 ( 673) hydrogen bonds : angle 4.68513 ( 1989) link_BETA1-4 : bond 0.00362 ( 2) link_BETA1-4 : angle 1.82625 ( 6) link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.54384 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8658 (t0) cc_final: 0.8408 (t70) REVERT: A 530 ARG cc_start: 0.6914 (mmt180) cc_final: 0.6691 (mmt180) REVERT: A 534 PHE cc_start: 0.8521 (m-80) cc_final: 0.8193 (m-10) REVERT: A 542 ASN cc_start: 0.9402 (OUTLIER) cc_final: 0.8596 (t0) REVERT: A 632 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7608 (tptp) REVERT: A 635 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8308 (tm-30) REVERT: A 978 MET cc_start: 0.8514 (tmt) cc_final: 0.8205 (tmm) REVERT: A 1571 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 1672 MET cc_start: 0.8849 (tmm) cc_final: 0.8600 (tmm) outliers start: 19 outliers final: 15 residues processed: 144 average time/residue: 0.1598 time to fit residues: 36.4719 Evaluate side-chains 140 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 522 TRP Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1359 THR Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1658 PHE Chi-restraints excluded: chain A residue 1748 HIS Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.087912 restraints weight = 68908.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091487 restraints weight = 25310.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.093787 restraints weight = 13876.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095227 restraints weight = 9471.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.095943 restraints weight = 7430.610| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10456 Z= 0.279 Angle : 0.559 5.399 14286 Z= 0.311 Chirality : 0.039 0.189 1620 Planarity : 0.004 0.034 1807 Dihedral : 5.193 59.649 1657 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.99 (0.23), residues: 1320 helix: 2.20 (0.17), residues: 866 sheet: -1.29 (0.70), residues: 53 loop : -0.24 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1601 TYR 0.016 0.001 TYR A1292 PHE 0.016 0.002 PHE A1475 TRP 0.010 0.001 TRP A 625 HIS 0.005 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00600 (10451) covalent geometry : angle 0.55808 (14273) SS BOND : bond 0.00510 ( 2) SS BOND : angle 0.67799 ( 4) hydrogen bonds : bond 0.04961 ( 673) hydrogen bonds : angle 4.62690 ( 1989) link_BETA1-4 : bond 0.00393 ( 2) link_BETA1-4 : angle 1.64067 ( 6) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 1.60859 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8666 (t0) cc_final: 0.8454 (t70) REVERT: A 530 ARG cc_start: 0.6885 (mmt180) cc_final: 0.6678 (mmt180) REVERT: A 534 PHE cc_start: 0.8528 (m-80) cc_final: 0.8185 (m-10) REVERT: A 542 ASN cc_start: 0.8765 (t0) cc_final: 0.8408 (t0) REVERT: A 632 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7543 (tptp) REVERT: A 635 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 978 MET cc_start: 0.8526 (tmt) cc_final: 0.8199 (tmm) REVERT: A 1571 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8078 (t80) REVERT: A 1672 MET cc_start: 0.8887 (tmm) cc_final: 0.8625 (tmm) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.1639 time to fit residues: 35.7302 Evaluate side-chains 143 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1359 THR Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1444 ARG Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1748 HIS Chi-restraints excluded: chain A residue 1749 VAL Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.088727 restraints weight = 67834.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.092332 restraints weight = 24843.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094654 restraints weight = 13542.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096129 restraints weight = 9258.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096761 restraints weight = 7226.069| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10456 Z= 0.132 Angle : 0.490 5.158 14286 Z= 0.261 Chirality : 0.037 0.181 1620 Planarity : 0.003 0.035 1807 Dihedral : 4.969 59.721 1657 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.66 % Allowed : 13.58 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.23), residues: 1320 helix: 2.50 (0.17), residues: 864 sheet: -1.13 (0.71), residues: 53 loop : -0.05 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 649 TYR 0.012 0.001 TYR A1292 PHE 0.018 0.001 PHE A1311 TRP 0.010 0.001 TRP A 224 HIS 0.004 0.001 HIS A1654 Details of bonding type rmsd covalent geometry : bond 0.00277 (10451) covalent geometry : angle 0.48865 (14273) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.24215 ( 4) hydrogen bonds : bond 0.04578 ( 673) hydrogen bonds : angle 4.24176 ( 1989) link_BETA1-4 : bond 0.00335 ( 2) link_BETA1-4 : angle 1.41681 ( 6) link_NAG-ASN : bond 0.00133 ( 1) link_NAG-ASN : angle 1.22672 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 PHE cc_start: 0.8465 (m-80) cc_final: 0.8112 (m-10) REVERT: A 542 ASN cc_start: 0.8907 (t0) cc_final: 0.8307 (t0) REVERT: A 635 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 978 MET cc_start: 0.8512 (tmt) cc_final: 0.8172 (tmm) REVERT: A 1571 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8008 (t80) REVERT: A 1672 MET cc_start: 0.8850 (tmm) cc_final: 0.8577 (tmm) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 0.1673 time to fit residues: 36.0900 Evaluate side-chains 142 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 522 TRP Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1658 PHE Chi-restraints excluded: chain A residue 1748 HIS Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.089547 restraints weight = 67882.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093171 restraints weight = 24894.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095508 restraints weight = 13640.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096741 restraints weight = 9314.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097807 restraints weight = 7498.134| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10456 Z= 0.171 Angle : 0.504 6.663 14286 Z= 0.271 Chirality : 0.037 0.178 1620 Planarity : 0.003 0.036 1807 Dihedral : 4.922 59.708 1657 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.66 % Allowed : 13.47 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.23), residues: 1320 helix: 2.54 (0.17), residues: 865 sheet: -1.17 (0.70), residues: 53 loop : -0.04 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1444 TYR 0.012 0.001 TYR A1292 PHE 0.016 0.001 PHE A1311 TRP 0.008 0.001 TRP A 625 HIS 0.004 0.001 HIS A1192 Details of bonding type rmsd covalent geometry : bond 0.00367 (10451) covalent geometry : angle 0.50303 (14273) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.31109 ( 4) hydrogen bonds : bond 0.04547 ( 673) hydrogen bonds : angle 4.26448 ( 1989) link_BETA1-4 : bond 0.00304 ( 2) link_BETA1-4 : angle 1.47234 ( 6) link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 1.25741 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 141 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue THR 269 is missing expected H atoms. Skipping. Residue THR 272 is missing expected H atoms. Skipping. Residue LEU 273 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 373 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue LYS 386 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue SER 461 is missing expected H atoms. Skipping. Residue SER 471 is missing expected H atoms. Skipping. Residue LEU 498 is missing expected H atoms. Skipping. Residue VAL 509 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue VAL 518 is missing expected H atoms. Skipping. Residue LYS 521 is missing expected H atoms. Skipping. Residue SER 529 is missing expected H atoms. Skipping. Residue LEU 543 is missing expected H atoms. Skipping. Residue TYR 552 is missing expected H atoms. Skipping. Residue TYR 558 is missing expected H atoms. Skipping. Residue THR 560 is missing expected H atoms. Skipping. Residue VAL 564 is missing expected H atoms. Skipping. Residue TYR 592 is missing expected H atoms. Skipping. Residue MET 593 is missing expected H atoms. Skipping. Residue LYS 594 is missing expected H atoms. Skipping. Residue LYS 595 is missing expected H atoms. Skipping. Residue SER 596 is missing expected H atoms. Skipping. Residue THR 597 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue THR 701 is missing expected H atoms. Skipping. Residue SER 704 is missing expected H atoms. Skipping. Residue LYS 707 is missing expected H atoms. Skipping. Residue SER 708 is missing expected H atoms. Skipping. Residue LEU 711 is missing expected H atoms. Skipping. Residue ILE 713 is missing expected H atoms. Skipping. Residue MET 839 is missing expected H atoms. Skipping. Residue LEU 857 is missing expected H atoms. Skipping. Residue ILE 861 is missing expected H atoms. Skipping. Residue VAL 870 is missing expected H atoms. Skipping. Residue THR 871 is missing expected H atoms. Skipping. Residue LEU 873 is missing expected H atoms. Skipping. Residue LEU 879 is missing expected H atoms. Skipping. Residue VAL 882 is missing expected H atoms. Skipping. Residue VAL 888 is missing expected H atoms. Skipping. Residue LYS 889 is missing expected H atoms. Skipping. Residue TYR 935 is missing expected H atoms. Skipping. Residue LEU 937 is missing expected H atoms. Skipping. Residue ILE 941 is missing expected H atoms. Skipping. Residue LEU 990 is missing expected H atoms. Skipping. Residue LEU 1021 is missing expected H atoms. Skipping. Residue LEU 1039 is missing expected H atoms. Skipping. Residue THR 1040 is missing expected H atoms. Skipping. Residue ILE 1058 is missing expected H atoms. Skipping. Residue LYS 1082 is missing expected H atoms. Skipping. Residue VAL 1127 is missing expected H atoms. Skipping. Residue VAL 1130 is missing expected H atoms. Skipping. Residue THR 1143 is missing expected H atoms. Skipping. Residue THR 1178 is missing expected H atoms. Skipping. Residue LEU 1179 is missing expected H atoms. Skipping. Residue THR 1183 is missing expected H atoms. Skipping. Residue LEU 1184 is missing expected H atoms. Skipping. Residue SER 1185 is missing expected H atoms. Skipping. Residue LEU 1191 is missing expected H atoms. Skipping. Residue TYR 1193 is missing expected H atoms. Skipping. Residue SER 1211 is missing expected H atoms. Skipping. Residue LYS 1212 is missing expected H atoms. Skipping. Residue LYS 1215 is missing expected H atoms. Skipping. Residue LEU 1217 is missing expected H atoms. Skipping. Residue ILE 1223 is missing expected H atoms. Skipping. Residue LEU 1308 is missing expected H atoms. Skipping. Residue LYS 1334 is missing expected H atoms. Skipping. Residue LYS 1336 is missing expected H atoms. Skipping. Residue THR 1337 is missing expected H atoms. Skipping. Residue VAL 1374 is missing expected H atoms. Skipping. Residue VAL 1375 is missing expected H atoms. Skipping. Residue LEU 1378 is missing expected H atoms. Skipping. Residue ILE 1379 is missing expected H atoms. Skipping. Residue LEU 1383 is missing expected H atoms. Skipping. Residue LYS 1385 is missing expected H atoms. Skipping. Residue THR 1387 is missing expected H atoms. Skipping. Residue ILE 1436 is missing expected H atoms. Skipping. Residue SER 1448 is missing expected H atoms. Skipping. Residue SER 1480 is missing expected H atoms. Skipping. Residue SER 1481 is missing expected H atoms. Skipping. Residue VAL 1488 is missing expected H atoms. Skipping. Residue LEU 1501 is missing expected H atoms. Skipping. Residue ILE 1507 is missing expected H atoms. Skipping. Residue SER 1521 is missing expected H atoms. Skipping. Residue ILE 1523 is missing expected H atoms. Skipping. Residue TYR 1525 is missing expected H atoms. Skipping. Residue VAL 1526 is missing expected H atoms. Skipping. Residue MET 1528 is missing expected H atoms. Skipping. Residue SER 1529 is missing expected H atoms. Skipping. Residue THR 1558 is missing expected H atoms. Skipping. Residue LEU 1560 is missing expected H atoms. Skipping. Residue ILE 1561 is missing expected H atoms. Skipping. Residue MET 1562 is missing expected H atoms. Skipping. Residue ILE 1565 is missing expected H atoms. Skipping. Residue ILE 1566 is missing expected H atoms. Skipping. Residue LYS 1589 is missing expected H atoms. Skipping. Residue VAL 1599 is missing expected H atoms. Skipping. Residue MET 1642 is missing expected H atoms. Skipping. Residue VAL 1651 is missing expected H atoms. Skipping. Residue VAL 1663 is missing expected H atoms. Skipping. Residue THR 1678 is missing expected H atoms. Skipping. Residue THR 1691 is missing expected H atoms. Skipping. Residue LEU 1693 is missing expected H atoms. Skipping. Residue MET 1694 is missing expected H atoms. Skipping. Residue LEU 1695 is missing expected H atoms. Skipping. Residue LEU 1730 is missing expected H atoms. Skipping. Residue THR 1731 is missing expected H atoms. Skipping. Residue VAL 1745 is missing expected H atoms. Skipping. Residue LEU 1751 is missing expected H atoms. Skipping. Residue LEU 1755 is missing expected H atoms. Skipping. Residue LEU 1757 is missing expected H atoms. Skipping. Residue ILE 1759 is missing expected H atoms. Skipping. Residue ILE 1760 is missing expected H atoms. Skipping. Residue LYS 1762 is missing expected H atoms. Skipping. Residue ILE 1763 is missing expected H atoms. Skipping. Residue LYS 1765 is missing expected H atoms. Skipping. Residue ILE 1769 is missing expected H atoms. Skipping. Residue MET 1770 is missing expected H atoms. Skipping. Residue LEU 1771 is missing expected H atoms. Skipping. Residue LEU 1774 is missing expected H atoms. Skipping. Residue LYS 1775 is missing expected H atoms. Skipping. Residue SER 1777 is missing expected H atoms. Skipping. Residue ILE 1780 is missing expected H atoms. Skipping. Residue SER 1786 is missing expected H atoms. Skipping. Residue LEU 1787 is missing expected H atoms. Skipping. Residue LYS 1788 is missing expected H atoms. Skipping. Residue THR 1790 is missing expected H atoms. Skipping. Residue LEU 1792 is missing expected H atoms. Skipping. Residue LYS 1794 is missing expected H atoms. Skipping. Residue MET 1796 is missing expected H atoms. Skipping. Residue LYS 1799 is missing expected H atoms. Skipping. Residue SER 1802 is missing expected H atoms. Skipping. Residue ILE 1810 is missing expected H atoms. Skipping. Residue LYS 1824 is missing expected H atoms. Skipping. Residue LYS 1827 is missing expected H atoms. Skipping. Residue VAL 1836 is missing expected H atoms. Skipping. Residue VAL 1837 is missing expected H atoms. Skipping. Residue ILE 1844 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue THR 1847 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 PHE cc_start: 0.8465 (m-80) cc_final: 0.8121 (m-10) REVERT: A 542 ASN cc_start: 0.9070 (t0) cc_final: 0.8156 (t0) REVERT: A 635 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 978 MET cc_start: 0.8511 (tmt) cc_final: 0.8156 (tmm) REVERT: A 1571 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 1672 MET cc_start: 0.8837 (tmm) cc_final: 0.8578 (tmm) outliers start: 15 outliers final: 14 residues processed: 140 average time/residue: 0.1609 time to fit residues: 35.8178 Evaluate side-chains 142 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 522 TRP Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1365 VAL Chi-restraints excluded: chain A residue 1367 TRP Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1492 HIS Chi-restraints excluded: chain A residue 1571 TYR Chi-restraints excluded: chain A residue 1604 ILE Chi-restraints excluded: chain A residue 1658 PHE Chi-restraints excluded: chain A residue 1748 HIS Chi-restraints excluded: chain A residue 1797 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089822 restraints weight = 67506.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093440 restraints weight = 24441.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095708 restraints weight = 13222.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096932 restraints weight = 9027.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097975 restraints weight = 7263.546| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10456 Z= 0.120 Angle : 0.484 6.841 14286 Z= 0.254 Chirality : 0.037 0.180 1620 Planarity : 0.003 0.036 1807 Dihedral : 4.819 58.253 1657 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.55 % Allowed : 13.47 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.23), residues: 1320 helix: 2.63 (0.17), residues: 867 sheet: -1.03 (0.71), residues: 53 loop : 0.08 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1444 TYR 0.012 0.001 TYR A1292 PHE 0.016 0.001 PHE A1311 TRP 0.009 0.001 TRP A 224 HIS 0.003 0.001 HIS A1654 Details of bonding type rmsd covalent geometry : bond 0.00249 (10451) covalent geometry : angle 0.48353 (14273) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.18327 ( 4) hydrogen bonds : bond 0.04354 ( 673) hydrogen bonds : angle 4.11554 ( 1989) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.40889 ( 6) link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.12266 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.13 seconds wall clock time: 49 minutes 16.51 seconds (2956.51 seconds total)