Starting phenix.real_space_refine on Thu Jun 4 12:15:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vxz_65446/06_2026/9vxz_65446.map" } resolution = 2.68 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= 0.000 sd= 0.014 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 Zn 1 6.06 5 S 63 5.16 5 C 8005 2.51 5 N 2177 2.21 5 O 2307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1255, 10082 Classifications: {'peptide': 1255} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1202} Chain breaks: 6 Chain: "B" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1159 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain breaks: 2 Chain: "C" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 372 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 514 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain breaks: 1 Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8770 SG CYS A1177 24.261 76.298 124.908 1.00 70.90 S ATOM 8791 SG CYS A1180 25.023 80.056 124.707 1.00 77.74 S Time building chain proxies: 3.22, per 1000 atoms: 0.26 Number of scatterers: 12553 At special positions: 0 Unit cell: (95.7076, 126.031, 156.354, 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) Zn 1 29.99 S 63 16.00 O 2307 8.00 N 2177 7.00 C 8005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 599.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" NE2 HIS A1364 " pdb="ZN ZN A2201 " - pdb=" ND1 HIS A1362 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1180 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1177 " Number of angles added : 1 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 7 sheets defined 60.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.929A pdb=" N ILE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.587A pdb=" N GLN A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 90 through 96 removed outlier: 3.644A pdb=" N ASN A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 134 removed outlier: 3.697A pdb=" N VAL A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LYS A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 removed outlier: 3.867A pdb=" N LYS A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 224 through 248 Processing helix chain 'A' and resid 251 through 273 removed outlier: 4.076A pdb=" N GLY A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.736A pdb=" N ILE A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.899A pdb=" N HIS A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.541A pdb=" N TYR A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.746A pdb=" N THR A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 347' Processing helix chain 'A' and resid 348 through 352 removed outlier: 3.512A pdb=" N SER A 351 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.603A pdb=" N ALA A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 472 through 480 removed outlier: 3.847A pdb=" N TRP A 476 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASP A 477 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 479 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.685A pdb=" N VAL A 517 " --> pdb=" O MET A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 550 through 567 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 672 through 688 removed outlier: 5.359A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N PHE A 679 " --> pdb=" O THR A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 743 through 762 Proline residue: A 753 - end of helix Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.504A pdb=" N ASP A 802 " --> pdb=" O ARG A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 851 removed outlier: 4.317A pdb=" N SER A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 916 through 923 Processing helix chain 'A' and resid 923 through 933 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 955 through 970 Processing helix chain 'A' and resid 975 through 983 removed outlier: 3.891A pdb=" N HIS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1024 Processing helix chain 'A' and resid 1038 through 1051 Processing helix chain 'A' and resid 1056 through 1067 Processing helix chain 'A' and resid 1067 through 1079 Processing helix chain 'A' and resid 1082 through 1093 Processing helix chain 'A' and resid 1096 through 1105 Processing helix chain 'A' and resid 1105 through 1119 removed outlier: 3.665A pdb=" N GLU A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1177 through 1183 removed outlier: 3.648A pdb=" N CYS A1182 " --> pdb=" O VAL A1178 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A1183 " --> pdb=" O ILE A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1250 Processing helix chain 'A' and resid 1254 through 1264 removed outlier: 3.738A pdb=" N GLU A1258 " --> pdb=" O SER A1254 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N TRP A1260 " --> pdb=" O TRP A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1278 Processing helix chain 'A' and resid 1304 through 1309 removed outlier: 3.984A pdb=" N ARG A1309 " --> pdb=" O VAL A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.752A pdb=" N LEU A1338 " --> pdb=" O GLN A1334 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A1339 " --> pdb=" O GLN A1335 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A1340 " --> pdb=" O GLY A1336 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 368 Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 474 through 487 removed outlier: 3.676A pdb=" N ARG B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 506 Processing helix chain 'C' and resid 326 through 370 Processing helix chain 'D' and resid 326 through 374 Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.821A pdb=" N ASP D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 368 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.450A pdb=" N SER A 83 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR A 222 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS A 219 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 381 removed outlier: 7.714A pdb=" N ALA E 373 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE B 398 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.542A pdb=" N ARG A 447 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 548 Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 770 removed outlier: 3.591A pdb=" N ARG A 765 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 836 through 838 removed outlier: 3.744A pdb=" N ILE A 836 " --> pdb=" O VAL A 843 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 841 " --> pdb=" O TYR A 838 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1166 through 1171 703 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4085 1.34 - 1.46: 2003 1.46 - 1.57: 6600 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 12792 Sorted by residual: bond pdb=" CG LEU B 342 " pdb=" CD2 LEU B 342 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" C ILE A 918 " pdb=" N PRO A 919 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.28e+00 bond pdb=" CA PHE A 269 " pdb=" C PHE A 269 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.10e+00 bond pdb=" CG1 ILE E 333 " pdb=" CD1 ILE E 333 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 9.97e-01 bond pdb=" CB THR A 874 " pdb=" CG2 THR A 874 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.56e-01 ... (remaining 12787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 17234 3.45 - 6.90: 45 6.90 - 10.36: 5 10.36 - 13.81: 0 13.81 - 17.26: 1 Bond angle restraints: 17285 Sorted by residual: angle pdb=" CA LEU B 342 " pdb=" CB LEU B 342 " pdb=" CG LEU B 342 " ideal model delta sigma weight residual 116.30 133.56 -17.26 3.50e+00 8.16e-02 2.43e+01 angle pdb=" N GLY A 569 " pdb=" CA GLY A 569 " pdb=" C GLY A 569 " ideal model delta sigma weight residual 113.18 105.57 7.61 2.37e+00 1.78e-01 1.03e+01 angle pdb=" C LEU B 341 " pdb=" N LEU B 342 " pdb=" CA LEU B 342 " ideal model delta sigma weight residual 121.14 115.64 5.50 1.75e+00 3.27e-01 9.87e+00 angle pdb=" CB ILE E 333 " pdb=" CG1 ILE E 333 " pdb=" CD1 ILE E 333 " ideal model delta sigma weight residual 113.80 120.27 -6.47 2.10e+00 2.27e-01 9.50e+00 angle pdb=" CA LEU E 336 " pdb=" CB LEU E 336 " pdb=" CG LEU E 336 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 ... (remaining 17280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 7145 15.70 - 31.41: 525 31.41 - 47.11: 100 47.11 - 62.81: 12 62.81 - 78.51: 1 Dihedral angle restraints: 7783 sinusoidal: 3193 harmonic: 4590 Sorted by residual: dihedral pdb=" CA ILE A 568 " pdb=" C ILE A 568 " pdb=" N GLY A 569 " pdb=" CA GLY A 569 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TRP A1256 " pdb=" C TRP A1256 " pdb=" N ASN A1257 " pdb=" CA ASN A1257 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ILE A 337 " pdb=" C ILE A 337 " pdb=" N PHE A 338 " pdb=" CA PHE A 338 " ideal model delta harmonic sigma weight residual 180.00 -164.49 -15.51 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 7780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1314 0.036 - 0.071: 497 0.071 - 0.107: 115 0.107 - 0.143: 47 0.143 - 0.179: 5 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CB ILE E 332 " pdb=" CA ILE E 332 " pdb=" CG1 ILE E 332 " pdb=" CG2 ILE E 332 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CA LEU B 342 " pdb=" N LEU B 342 " pdb=" C LEU B 342 " pdb=" CB LEU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB VAL A 446 " pdb=" CA VAL A 446 " pdb=" CG1 VAL A 446 " pdb=" CG2 VAL A 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 1975 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 391 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 392 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 392 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 392 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 933 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 934 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 934 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 934 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1395 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.47e+00 pdb=" N PRO A1396 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1396 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1396 " 0.026 5.00e-02 4.00e+02 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5929 2.99 - 3.47: 12850 3.47 - 3.95: 21102 3.95 - 4.42: 24454 4.42 - 4.90: 38384 Nonbonded interactions: 102719 Sorted by model distance: nonbonded pdb=" N GLY A 569 " pdb=" N LYS A 570 " model vdw 2.514 2.560 nonbonded pdb=" N ASP A 728 " pdb=" O ASP A 728 " model vdw 2.628 2.496 nonbonded pdb=" N ILE B 325 " pdb=" N HIS B 326 " model vdw 2.629 2.560 nonbonded pdb=" N VAL A 916 " pdb=" N VAL A 917 " model vdw 2.635 2.560 nonbonded pdb=" N ILE A1398 " pdb=" N TYR A1399 " model vdw 2.636 2.560 ... (remaining 102714 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and resid 325 through 371) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.060 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:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 0.041 12796 Z= 0.133 Angle : 0.601 17.262 17286 Z= 0.306 Chirality : 0.042 0.179 1978 Planarity : 0.005 0.051 2183 Dihedral : 11.151 78.514 4809 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1544 helix: 0.98 (0.17), residues: 866 sheet: 0.77 (0.57), residues: 87 loop : -0.80 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 371 TYR 0.012 0.001 TYR A 886 PHE 0.027 0.002 PHE A 392 TRP 0.016 0.001 TRP A1189 HIS 0.008 0.001 HIS A1174 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12792) covalent geometry : angle 0.60039 / 0.31 (17285) hydrogen bonds : bond 0.11396 / 7.52 ( 703) hydrogen bonds : angle 5.04635 / 3.60 ( 2037) metal coordination : bond 0.00658 / 0.33 ( 4) metal coordination : angle 3.14778 / 1.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8295 (mttt) cc_final: 0.8083 (mtpm) REVERT: A 114 ASN cc_start: 0.8169 (m-40) cc_final: 0.7876 (m-40) REVERT: A 284 GLU cc_start: 0.7476 (tt0) cc_final: 0.7259 (tt0) REVERT: A 373 TYR cc_start: 0.8398 (m-80) cc_final: 0.7947 (m-80) REVERT: A 400 TYR cc_start: 0.8665 (t80) cc_final: 0.8392 (t80) REVERT: A 423 ASN cc_start: 0.8367 (m-40) cc_final: 0.8053 (m-40) REVERT: A 427 SER cc_start: 0.8313 (m) cc_final: 0.8018 (p) REVERT: A 463 TYR cc_start: 0.8123 (m-80) cc_final: 0.7855 (m-80) REVERT: A 504 ASN cc_start: 0.7810 (m-40) cc_final: 0.7579 (t0) REVERT: A 666 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7622 (mmtt) REVERT: A 669 LEU cc_start: 0.8647 (mt) cc_final: 0.8362 (mt) REVERT: A 798 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8118 (ttp80) REVERT: A 859 THR cc_start: 0.8242 (p) cc_final: 0.8015 (p) REVERT: A 877 LYS cc_start: 0.8449 (tttt) cc_final: 0.8203 (ttmm) REVERT: A 1013 LEU cc_start: 0.8192 (tp) cc_final: 0.7914 (tt) REVERT: A 1065 ASP cc_start: 0.7768 (t0) cc_final: 0.7546 (t0) REVERT: A 1108 TYR cc_start: 0.8514 (t80) cc_final: 0.7556 (t80) REVERT: A 1178 VAL cc_start: 0.7965 (t) cc_final: 0.7746 (p) REVERT: A 1240 ARG cc_start: 0.8455 (tpt170) cc_final: 0.8238 (tpt90) REVERT: B 371 MET cc_start: 0.7265 (mmp) cc_final: 0.7062 (mmp) REVERT: B 411 LYS cc_start: 0.7457 (mttt) cc_final: 0.7122 (mttt) REVERT: B 433 LEU cc_start: 0.8465 (tp) cc_final: 0.8211 (mt) REVERT: B 455 ASP cc_start: 0.7818 (p0) cc_final: 0.7585 (p0) REVERT: B 473 LEU cc_start: 0.8151 (mt) cc_final: 0.7758 (mp) REVERT: B 484 LEU cc_start: 0.8560 (mt) cc_final: 0.8238 (mp) REVERT: B 496 LYS cc_start: 0.8626 (mttt) cc_final: 0.8370 (mttt) REVERT: B 500 MET cc_start: 0.8309 (ttp) cc_final: 0.8108 (tmm) REVERT: C 371 MET cc_start: 0.5358 (mpp) cc_final: 0.5020 (mpm) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.6737 time to fit residues: 263.2990 Evaluate side-chains 324 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 694 GLN A 892 ASN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 ASN A1186 ASN A1335 GLN A1401 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121094 restraints weight = 17745.512| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.90 r_work: 0.3471 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12796 Z= 0.178 Angle : 0.539 11.132 17286 Z= 0.274 Chirality : 0.041 0.149 1978 Planarity : 0.004 0.048 2183 Dihedral : 4.064 20.250 1711 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.64 % Allowed : 9.70 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.22), residues: 1544 helix: 1.63 (0.18), residues: 873 sheet: 0.82 (0.56), residues: 92 loop : -0.66 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1389 TYR 0.014 0.002 TYR A 336 PHE 0.027 0.002 PHE A 546 TRP 0.018 0.001 TRP A 440 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (12792) covalent geometry : angle 0.53875 / 0.27 (17285) hydrogen bonds : bond 0.04255 / 2.86 ( 703) hydrogen bonds : angle 4.00726 / 2.89 ( 2037) metal coordination : bond 0.00665 / 0.34 ( 4) metal coordination : angle 3.54777 / 1.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8204 (mpt180) cc_final: 0.7990 (mpt180) REVERT: A 114 ASN cc_start: 0.8098 (m-40) cc_final: 0.7881 (m-40) REVERT: A 284 GLU cc_start: 0.7489 (tt0) cc_final: 0.7276 (tt0) REVERT: A 400 TYR cc_start: 0.8707 (t80) cc_final: 0.8077 (t80) REVERT: A 423 ASN cc_start: 0.8436 (m-40) cc_final: 0.8081 (m-40) REVERT: A 427 SER cc_start: 0.8373 (m) cc_final: 0.8112 (p) REVERT: A 562 ASN cc_start: 0.8601 (t0) cc_final: 0.8361 (t160) REVERT: A 666 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7435 (mmtt) REVERT: A 809 GLN cc_start: 0.8044 (tp40) cc_final: 0.7805 (tp-100) REVERT: A 859 THR cc_start: 0.8202 (p) cc_final: 0.7938 (p) REVERT: A 877 LYS cc_start: 0.8535 (tttt) cc_final: 0.8276 (ttmm) REVERT: A 916 VAL cc_start: 0.8011 (p) cc_final: 0.7755 (m) REVERT: A 997 ASP cc_start: 0.7414 (t0) cc_final: 0.7214 (t0) REVERT: A 1040 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 1065 ASP cc_start: 0.7818 (t0) cc_final: 0.7584 (t0) REVERT: A 1144 MET cc_start: 0.8626 (mmm) cc_final: 0.8322 (mmm) REVERT: A 1157 LEU cc_start: 0.7873 (mt) cc_final: 0.7593 (mt) REVERT: A 1181 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 1273 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7152 (mp0) REVERT: A 1385 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7681 (mmtt) REVERT: A 1399 TYR cc_start: 0.8194 (t80) cc_final: 0.7957 (t80) REVERT: B 371 MET cc_start: 0.7303 (mmp) cc_final: 0.7018 (mmp) REVERT: B 482 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8157 (mmt) REVERT: B 500 MET cc_start: 0.8340 (ttp) cc_final: 0.8133 (tmm) REVERT: C 371 MET cc_start: 0.5257 (mpp) cc_final: 0.4881 (mpm) outliers start: 23 outliers final: 6 residues processed: 333 average time/residue: 0.6933 time to fit residues: 248.2813 Evaluate side-chains 306 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 299 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 105 optimal weight: 0.5980 chunk 25 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 126 GLN A 504 ASN A 697 HIS A 845 GLN A1110 GLN A1124 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.143628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120940 restraints weight = 17738.923| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.90 r_work: 0.3461 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12796 Z= 0.169 Angle : 0.518 8.997 17286 Z= 0.262 Chirality : 0.041 0.143 1978 Planarity : 0.004 0.047 2183 Dihedral : 4.039 20.877 1711 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.85 % Allowed : 11.84 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.31 (0.22), residues: 1544 helix: 1.83 (0.18), residues: 874 sheet: 0.86 (0.58), residues: 92 loop : -0.63 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1389 TYR 0.013 0.002 TYR A 336 PHE 0.019 0.002 PHE A 546 TRP 0.015 0.001 TRP A 440 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (12792) covalent geometry : angle 0.51769 / 0.26 (17285) hydrogen bonds : bond 0.04085 / 2.75 ( 703) hydrogen bonds : angle 3.92801 / 2.83 ( 2037) metal coordination : bond 0.00579 / 0.29 ( 4) metal coordination : angle 1.85468 / 0.98 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 313 time to evaluate : 0.525 Fit side-chains REVERT: A 284 GLU cc_start: 0.7489 (tt0) cc_final: 0.7269 (tt0) REVERT: A 354 ARG cc_start: 0.7766 (mtt180) cc_final: 0.7432 (mtt180) REVERT: A 400 TYR cc_start: 0.8669 (t80) cc_final: 0.8224 (t80) REVERT: A 401 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8236 (ttp80) REVERT: A 423 ASN cc_start: 0.8446 (m-40) cc_final: 0.8142 (m-40) REVERT: A 427 SER cc_start: 0.8409 (m) cc_final: 0.8140 (p) REVERT: A 562 ASN cc_start: 0.8623 (t0) cc_final: 0.8392 (t160) REVERT: A 666 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7409 (mmtt) REVERT: A 809 GLN cc_start: 0.8019 (tp40) cc_final: 0.7787 (tp-100) REVERT: A 859 THR cc_start: 0.8211 (p) cc_final: 0.7944 (p) REVERT: A 877 LYS cc_start: 0.8534 (tttt) cc_final: 0.8301 (tttp) REVERT: A 997 ASP cc_start: 0.7401 (t0) cc_final: 0.7185 (t0) REVERT: A 1040 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 1041 GLU cc_start: 0.7646 (pt0) cc_final: 0.7246 (pt0) REVERT: A 1108 TYR cc_start: 0.8350 (t80) cc_final: 0.7915 (t80) REVERT: A 1128 ASP cc_start: 0.7491 (p0) cc_final: 0.7149 (p0) REVERT: A 1157 LEU cc_start: 0.7762 (mt) cc_final: 0.7522 (mt) REVERT: A 1166 MET cc_start: 0.8514 (mtm) cc_final: 0.8210 (mtt) REVERT: A 1181 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7123 (mt-10) REVERT: A 1273 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7188 (mp0) REVERT: A 1385 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7675 (mmtt) REVERT: B 371 MET cc_start: 0.7324 (mmp) cc_final: 0.7019 (mmp) REVERT: B 471 SER cc_start: 0.8421 (p) cc_final: 0.8191 (p) REVERT: B 482 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8163 (mmt) outliers start: 26 outliers final: 10 residues processed: 321 average time/residue: 0.7072 time to fit residues: 243.9340 Evaluate side-chains 315 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 303 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 724 LYS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 88 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 132 optimal weight: 0.5980 chunk 112 optimal weight: 0.2980 chunk 151 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 504 ASN A 771 GLN A1105 ASN A1110 GLN A1124 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120271 restraints weight = 17712.864| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.90 r_work: 0.3460 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12796 Z= 0.166 Angle : 0.522 14.129 17286 Z= 0.263 Chirality : 0.042 0.336 1978 Planarity : 0.004 0.046 2183 Dihedral : 4.010 20.516 1711 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.78 % Allowed : 14.05 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.44 (0.22), residues: 1544 helix: 1.94 (0.18), residues: 878 sheet: 0.98 (0.60), residues: 84 loop : -0.59 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 929 TYR 0.012 0.001 TYR A 336 PHE 0.028 0.002 PHE A 546 TRP 0.014 0.001 TRP A 440 HIS 0.004 0.001 HIS A1035 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (12792) covalent geometry : angle 0.52197 / 0.26 (17285) hydrogen bonds : bond 0.04038 / 2.72 ( 703) hydrogen bonds : angle 3.88944 / 2.80 ( 2037) metal coordination : bond 0.00521 / 0.26 ( 4) metal coordination : angle 1.63222 / 0.86 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 311 time to evaluate : 0.493 Fit side-chains REVERT: A 17 ASP cc_start: 0.7468 (p0) cc_final: 0.7239 (p0) REVERT: A 284 GLU cc_start: 0.7489 (tt0) cc_final: 0.7263 (tt0) REVERT: A 354 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7410 (mtt180) REVERT: A 400 TYR cc_start: 0.8667 (t80) cc_final: 0.8237 (t80) REVERT: A 401 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8349 (ttp80) REVERT: A 423 ASN cc_start: 0.8437 (m-40) cc_final: 0.8148 (m-40) REVERT: A 427 SER cc_start: 0.8402 (m) cc_final: 0.8131 (p) REVERT: A 562 ASN cc_start: 0.8608 (t0) cc_final: 0.8376 (t160) REVERT: A 666 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7352 (mmtt) REVERT: A 809 GLN cc_start: 0.8016 (tp40) cc_final: 0.7803 (tp-100) REVERT: A 859 THR cc_start: 0.8253 (p) cc_final: 0.8001 (p) REVERT: A 877 LYS cc_start: 0.8490 (tttt) cc_final: 0.8266 (tttp) REVERT: A 916 VAL cc_start: 0.8031 (p) cc_final: 0.7801 (m) REVERT: A 997 ASP cc_start: 0.7401 (t0) cc_final: 0.7156 (t0) REVERT: A 1041 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: A 1108 TYR cc_start: 0.8254 (t80) cc_final: 0.7964 (t80) REVERT: A 1128 ASP cc_start: 0.7394 (p0) cc_final: 0.7096 (p0) REVERT: A 1157 LEU cc_start: 0.7731 (mt) cc_final: 0.7527 (mt) REVERT: A 1181 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7091 (mt-10) REVERT: A 1273 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7183 (mp0) REVERT: A 1385 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7708 (mmtt) REVERT: B 471 SER cc_start: 0.8423 (p) cc_final: 0.8209 (p) REVERT: B 482 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8170 (mmt) outliers start: 25 outliers final: 10 residues processed: 319 average time/residue: 0.6914 time to fit residues: 237.0214 Evaluate side-chains 315 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 302 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 504 ASN A 771 GLN A 845 GLN A1105 ASN A1110 GLN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118954 restraints weight = 17803.922| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.91 r_work: 0.3441 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12796 Z= 0.246 Angle : 0.567 12.430 17286 Z= 0.287 Chirality : 0.044 0.193 1978 Planarity : 0.004 0.047 2183 Dihedral : 4.163 19.526 1711 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.57 % Allowed : 13.84 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.31 (0.22), residues: 1544 helix: 1.80 (0.17), residues: 883 sheet: 1.01 (0.59), residues: 89 loop : -0.62 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1389 TYR 0.015 0.002 TYR A1106 PHE 0.027 0.002 PHE A 546 TRP 0.016 0.002 TRP A 440 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (12792) covalent geometry : angle 0.56727 / 0.29 (17285) hydrogen bonds : bond 0.04455 / 3.00 ( 703) hydrogen bonds : angle 4.00429 / 2.87 ( 2037) metal coordination : bond 0.00781 / 0.39 ( 4) metal coordination : angle 0.78919 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7419 (p0) cc_final: 0.7211 (p0) REVERT: A 284 GLU cc_start: 0.7535 (tt0) cc_final: 0.7299 (tt0) REVERT: A 354 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7437 (mtt180) REVERT: A 372 LYS cc_start: 0.8280 (ptmt) cc_final: 0.8044 (pttm) REVERT: A 373 TYR cc_start: 0.8392 (m-80) cc_final: 0.8183 (m-80) REVERT: A 400 TYR cc_start: 0.8683 (t80) cc_final: 0.8223 (t80) REVERT: A 401 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8281 (ttp80) REVERT: A 423 ASN cc_start: 0.8471 (m-40) cc_final: 0.8177 (m-40) REVERT: A 427 SER cc_start: 0.8430 (m) cc_final: 0.8154 (p) REVERT: A 562 ASN cc_start: 0.8623 (t0) cc_final: 0.8404 (t160) REVERT: A 663 ASP cc_start: 0.7735 (t0) cc_final: 0.7526 (t0) REVERT: A 809 GLN cc_start: 0.8036 (tp40) cc_final: 0.7823 (tp-100) REVERT: A 859 THR cc_start: 0.8257 (p) cc_final: 0.8001 (p) REVERT: A 877 LYS cc_start: 0.8488 (tttt) cc_final: 0.8271 (tttp) REVERT: A 997 ASP cc_start: 0.7444 (t0) cc_final: 0.7183 (t0) REVERT: A 1013 LEU cc_start: 0.8470 (mt) cc_final: 0.8264 (tp) REVERT: A 1041 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7331 (pt0) REVERT: A 1065 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: A 1108 TYR cc_start: 0.8191 (t80) cc_final: 0.7939 (t80) REVERT: A 1128 ASP cc_start: 0.7344 (p0) cc_final: 0.7099 (p0) REVERT: A 1157 LEU cc_start: 0.7807 (mt) cc_final: 0.7541 (mt) REVERT: A 1166 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8132 (mtm) REVERT: A 1178 VAL cc_start: 0.7876 (t) cc_final: 0.7429 (p) REVERT: A 1181 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7105 (mt-10) REVERT: A 1273 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7286 (mp0) REVERT: A 1385 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7709 (mmtt) REVERT: B 482 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8150 (mmt) outliers start: 36 outliers final: 16 residues processed: 321 average time/residue: 0.7245 time to fit residues: 249.4842 Evaluate side-chains 322 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 301 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1041 GLU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1271 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 148 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 138 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 118 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 504 ASN A 771 GLN A1110 GLN A1124 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120583 restraints weight = 17611.211| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.90 r_work: 0.3464 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12796 Z= 0.144 Angle : 0.502 7.883 17286 Z= 0.256 Chirality : 0.040 0.150 1978 Planarity : 0.004 0.044 2183 Dihedral : 4.000 21.126 1711 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 16.26 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.22), residues: 1544 helix: 2.02 (0.18), residues: 883 sheet: 0.91 (0.60), residues: 84 loop : -0.55 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1389 TYR 0.014 0.001 TYR A1106 PHE 0.029 0.001 PHE A 546 TRP 0.011 0.001 TRP A 440 HIS 0.005 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (12792) covalent geometry : angle 0.50177 / 0.26 (17285) hydrogen bonds : bond 0.03911 / 2.63 ( 703) hydrogen bonds : angle 3.84755 / 2.76 ( 2037) metal coordination : bond 0.00449 / 0.23 ( 4) metal coordination : angle 1.45150 / 0.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 284 GLU cc_start: 0.7514 (tt0) cc_final: 0.7280 (tt0) REVERT: A 354 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7417 (mtt180) REVERT: A 400 TYR cc_start: 0.8637 (t80) cc_final: 0.8291 (t80) REVERT: A 423 ASN cc_start: 0.8455 (m-40) cc_final: 0.8172 (m-40) REVERT: A 427 SER cc_start: 0.8407 (m) cc_final: 0.8148 (p) REVERT: A 562 ASN cc_start: 0.8614 (t0) cc_final: 0.8388 (t160) REVERT: A 663 ASP cc_start: 0.7685 (t0) cc_final: 0.7459 (t0) REVERT: A 859 THR cc_start: 0.8238 (p) cc_final: 0.7965 (p) REVERT: A 877 LYS cc_start: 0.8480 (tttt) cc_final: 0.8254 (tttp) REVERT: A 916 VAL cc_start: 0.7996 (p) cc_final: 0.7744 (m) REVERT: A 997 ASP cc_start: 0.7387 (t0) cc_final: 0.7130 (t0) REVERT: A 1123 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7866 (mtm180) REVERT: A 1128 ASP cc_start: 0.7180 (p0) cc_final: 0.6927 (p0) REVERT: A 1157 LEU cc_start: 0.7744 (mt) cc_final: 0.7509 (mt) REVERT: A 1166 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8132 (mtm) REVERT: A 1178 VAL cc_start: 0.7851 (t) cc_final: 0.7384 (p) REVERT: A 1181 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 1273 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7162 (mp0) REVERT: A 1338 LEU cc_start: 0.8113 (mt) cc_final: 0.7909 (mt) REVERT: A 1385 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7713 (mmtt) REVERT: B 471 SER cc_start: 0.8413 (p) cc_final: 0.8205 (p) REVERT: B 482 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8152 (mmt) outliers start: 31 outliers final: 15 residues processed: 324 average time/residue: 0.6745 time to fit residues: 234.6114 Evaluate side-chains 321 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 304 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 104 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 771 GLN A 809 GLN A 870 ASN A1105 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.141875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119293 restraints weight = 17724.518| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.90 r_work: 0.3451 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12796 Z= 0.206 Angle : 0.546 8.115 17286 Z= 0.278 Chirality : 0.042 0.167 1978 Planarity : 0.004 0.047 2183 Dihedral : 4.062 19.352 1711 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.57 % Allowed : 16.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.39 (0.22), residues: 1544 helix: 1.91 (0.18), residues: 883 sheet: 0.86 (0.60), residues: 84 loop : -0.61 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1389 TYR 0.017 0.002 TYR A1108 PHE 0.029 0.002 PHE A 546 TRP 0.014 0.001 TRP A 440 HIS 0.004 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (12792) covalent geometry : angle 0.54615 / 0.28 (17285) hydrogen bonds : bond 0.04225 / 2.85 ( 703) hydrogen bonds : angle 3.92689 / 2.81 ( 2037) metal coordination : bond 0.00638 / 0.32 ( 4) metal coordination : angle 0.73507 / 0.39 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 311 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 114 ASN cc_start: 0.8138 (m-40) cc_final: 0.7927 (m-40) REVERT: A 284 GLU cc_start: 0.7548 (tt0) cc_final: 0.7309 (tt0) REVERT: A 354 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7424 (mtt180) REVERT: A 400 TYR cc_start: 0.8657 (t80) cc_final: 0.8255 (t80) REVERT: A 401 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8215 (ttp80) REVERT: A 411 LEU cc_start: 0.8658 (tp) cc_final: 0.8353 (tp) REVERT: A 423 ASN cc_start: 0.8458 (m-40) cc_final: 0.8164 (m-40) REVERT: A 427 SER cc_start: 0.8418 (m) cc_final: 0.8151 (p) REVERT: A 562 ASN cc_start: 0.8593 (t0) cc_final: 0.8358 (t160) REVERT: A 663 ASP cc_start: 0.7673 (t0) cc_final: 0.7432 (t0) REVERT: A 783 VAL cc_start: 0.8504 (m) cc_final: 0.8141 (p) REVERT: A 859 THR cc_start: 0.8248 (p) cc_final: 0.7998 (p) REVERT: A 877 LYS cc_start: 0.8479 (tttt) cc_final: 0.8256 (tttp) REVERT: A 997 ASP cc_start: 0.7412 (t0) cc_final: 0.7143 (t0) REVERT: A 1065 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: A 1112 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7936 (mtp85) REVERT: A 1128 ASP cc_start: 0.7047 (p0) cc_final: 0.6775 (p0) REVERT: A 1157 LEU cc_start: 0.7751 (mt) cc_final: 0.7508 (mt) REVERT: A 1166 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8167 (mtm) REVERT: A 1178 VAL cc_start: 0.7857 (t) cc_final: 0.7394 (p) REVERT: A 1181 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 1273 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7245 (mp0) REVERT: A 1338 LEU cc_start: 0.8180 (mt) cc_final: 0.7959 (mt) REVERT: A 1385 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7711 (mmtt) REVERT: B 471 SER cc_start: 0.8413 (p) cc_final: 0.8191 (p) REVERT: B 482 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8161 (mmt) outliers start: 36 outliers final: 16 residues processed: 323 average time/residue: 0.7254 time to fit residues: 250.9707 Evaluate side-chains 332 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain A residue 1271 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 771 GLN A 809 GLN A 870 ASN A1124 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119413 restraints weight = 17523.094| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.89 r_work: 0.3451 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12796 Z= 0.201 Angle : 0.546 7.791 17286 Z= 0.278 Chirality : 0.042 0.161 1978 Planarity : 0.004 0.047 2183 Dihedral : 4.061 20.478 1711 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.07 % Allowed : 16.90 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1544 helix: 1.93 (0.18), residues: 882 sheet: 0.80 (0.60), residues: 84 loop : -0.66 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1389 TYR 0.019 0.002 TYR A1106 PHE 0.028 0.002 PHE A 546 TRP 0.014 0.001 TRP A 440 HIS 0.007 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (12792) covalent geometry : angle 0.54603 / 0.28 (17285) hydrogen bonds : bond 0.04186 / 2.82 ( 703) hydrogen bonds : angle 3.91906 / 2.81 ( 2037) metal coordination : bond 0.00531 / 0.27 ( 4) metal coordination : angle 0.88805 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 0.508 Fit side-chains REVERT: A 284 GLU cc_start: 0.7540 (tt0) cc_final: 0.7276 (tt0) REVERT: A 354 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7424 (mtt180) REVERT: A 400 TYR cc_start: 0.8659 (t80) cc_final: 0.8293 (t80) REVERT: A 401 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8158 (ttp80) REVERT: A 411 LEU cc_start: 0.8655 (tp) cc_final: 0.8352 (tp) REVERT: A 423 ASN cc_start: 0.8454 (m-40) cc_final: 0.8157 (m-40) REVERT: A 427 SER cc_start: 0.8413 (m) cc_final: 0.8152 (p) REVERT: A 562 ASN cc_start: 0.8600 (t0) cc_final: 0.8362 (t160) REVERT: A 663 ASP cc_start: 0.7650 (t0) cc_final: 0.7399 (t0) REVERT: A 783 VAL cc_start: 0.8483 (m) cc_final: 0.8124 (p) REVERT: A 859 THR cc_start: 0.8268 (p) cc_final: 0.8021 (p) REVERT: A 877 LYS cc_start: 0.8467 (tttt) cc_final: 0.8249 (tttp) REVERT: A 997 ASP cc_start: 0.7417 (t0) cc_final: 0.7155 (t0) REVERT: A 1065 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: A 1079 LEU cc_start: 0.8291 (tt) cc_final: 0.8007 (tp) REVERT: A 1112 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7976 (mtp85) REVERT: A 1157 LEU cc_start: 0.7752 (mt) cc_final: 0.7534 (mt) REVERT: A 1178 VAL cc_start: 0.7849 (t) cc_final: 0.7340 (p) REVERT: A 1181 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7150 (mt-10) REVERT: A 1252 ASP cc_start: 0.7907 (p0) cc_final: 0.6617 (p0) REVERT: A 1273 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7252 (mp0) REVERT: A 1379 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6933 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7704 (mmtt) REVERT: B 471 SER cc_start: 0.8420 (p) cc_final: 0.8214 (p) REVERT: B 482 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8176 (mmt) REVERT: E 371 MET cc_start: 0.8044 (mtm) cc_final: 0.7770 (mmm) outliers start: 29 outliers final: 17 residues processed: 321 average time/residue: 0.7257 time to fit residues: 249.8817 Evaluate side-chains 323 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 303 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1271 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 771 GLN A 809 GLN A 870 ASN A1105 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119670 restraints weight = 17762.202| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.90 r_work: 0.3454 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12796 Z= 0.190 Angle : 0.543 7.813 17286 Z= 0.277 Chirality : 0.042 0.157 1978 Planarity : 0.004 0.048 2183 Dihedral : 4.026 19.860 1711 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.78 % Allowed : 17.19 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.40 (0.22), residues: 1544 helix: 1.94 (0.18), residues: 883 sheet: 0.72 (0.59), residues: 84 loop : -0.63 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1389 TYR 0.022 0.002 TYR A1106 PHE 0.029 0.002 PHE A 546 TRP 0.014 0.001 TRP A 440 HIS 0.007 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (12792) covalent geometry : angle 0.54305 / 0.28 (17285) hydrogen bonds : bond 0.04136 / 2.79 ( 703) hydrogen bonds : angle 3.90414 / 2.80 ( 2037) metal coordination : bond 0.00498 / 0.25 ( 4) metal coordination : angle 0.89983 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.538 Fit side-chains REVERT: A 13 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7836 (mt-10) REVERT: A 284 GLU cc_start: 0.7446 (tt0) cc_final: 0.7204 (tt0) REVERT: A 354 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7413 (mtt180) REVERT: A 400 TYR cc_start: 0.8658 (t80) cc_final: 0.8295 (t80) REVERT: A 401 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8163 (ttp80) REVERT: A 411 LEU cc_start: 0.8663 (tp) cc_final: 0.8369 (tp) REVERT: A 423 ASN cc_start: 0.8466 (m-40) cc_final: 0.8171 (m-40) REVERT: A 427 SER cc_start: 0.8410 (m) cc_final: 0.8155 (p) REVERT: A 562 ASN cc_start: 0.8595 (t0) cc_final: 0.8377 (t0) REVERT: A 663 ASP cc_start: 0.7649 (t0) cc_final: 0.7392 (t0) REVERT: A 783 VAL cc_start: 0.8494 (m) cc_final: 0.8138 (p) REVERT: A 859 THR cc_start: 0.8221 (p) cc_final: 0.7990 (p) REVERT: A 877 LYS cc_start: 0.8471 (tttt) cc_final: 0.8248 (tttp) REVERT: A 997 ASP cc_start: 0.7416 (t0) cc_final: 0.7160 (t0) REVERT: A 1011 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7662 (ttp-170) REVERT: A 1065 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: A 1079 LEU cc_start: 0.8256 (tt) cc_final: 0.8055 (tp) REVERT: A 1112 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7947 (mtp85) REVERT: A 1157 LEU cc_start: 0.7747 (mt) cc_final: 0.7521 (mt) REVERT: A 1166 MET cc_start: 0.8493 (mtm) cc_final: 0.8132 (mtm) REVERT: A 1178 VAL cc_start: 0.7861 (t) cc_final: 0.7361 (p) REVERT: A 1181 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 1252 ASP cc_start: 0.7905 (p0) cc_final: 0.6594 (p0) REVERT: A 1273 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7244 (mp0) REVERT: A 1379 ARG cc_start: 0.7158 (ttm-80) cc_final: 0.6942 (ttm-80) REVERT: A 1385 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7716 (mmtt) REVERT: B 482 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mmt) REVERT: E 371 MET cc_start: 0.8053 (mtm) cc_final: 0.7783 (mmm) outliers start: 25 outliers final: 17 residues processed: 314 average time/residue: 0.7274 time to fit residues: 244.9734 Evaluate side-chains 320 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1271 LEU Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 25 optimal weight: 0.0030 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 96 optimal weight: 0.0070 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 771 GLN A 809 GLN A 870 ASN A1105 ASN A1124 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121286 restraints weight = 17844.145| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.90 r_work: 0.3470 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12796 Z= 0.138 Angle : 0.526 7.260 17286 Z= 0.267 Chirality : 0.040 0.151 1978 Planarity : 0.004 0.053 2183 Dihedral : 3.936 21.120 1711 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.36 % Allowed : 17.83 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.55 (0.22), residues: 1544 helix: 2.03 (0.18), residues: 885 sheet: 0.93 (0.59), residues: 82 loop : -0.55 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1389 TYR 0.021 0.001 TYR A1106 PHE 0.031 0.001 PHE A 546 TRP 0.011 0.001 TRP A 440 HIS 0.007 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (12792) covalent geometry : angle 0.52576 / 0.27 (17285) hydrogen bonds : bond 0.03834 / 2.58 ( 703) hydrogen bonds : angle 3.82510 / 2.75 ( 2037) metal coordination : bond 0.00421 / 0.21 ( 4) metal coordination : angle 1.31691 / 0.69 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7825 (mt-10) REVERT: A 284 GLU cc_start: 0.7399 (tt0) cc_final: 0.7164 (tt0) REVERT: A 354 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7366 (mtt180) REVERT: A 400 TYR cc_start: 0.8636 (t80) cc_final: 0.8311 (t80) REVERT: A 401 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8337 (ttp80) REVERT: A 411 LEU cc_start: 0.8627 (tp) cc_final: 0.8346 (tp) REVERT: A 423 ASN cc_start: 0.8452 (m-40) cc_final: 0.8166 (m-40) REVERT: A 427 SER cc_start: 0.8387 (m) cc_final: 0.8144 (p) REVERT: A 465 LYS cc_start: 0.7766 (mptt) cc_final: 0.7527 (mmtt) REVERT: A 562 ASN cc_start: 0.8570 (t0) cc_final: 0.8329 (t160) REVERT: A 663 ASP cc_start: 0.7624 (t0) cc_final: 0.7367 (t0) REVERT: A 781 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7991 (tttm) REVERT: A 859 THR cc_start: 0.8266 (p) cc_final: 0.8032 (p) REVERT: A 877 LYS cc_start: 0.8457 (tttt) cc_final: 0.8235 (tttp) REVERT: A 997 ASP cc_start: 0.7374 (t0) cc_final: 0.7112 (t0) REVERT: A 1065 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: A 1079 LEU cc_start: 0.8243 (tt) cc_final: 0.8038 (tp) REVERT: A 1112 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7961 (mtp85) REVERT: A 1178 VAL cc_start: 0.7850 (t) cc_final: 0.7359 (p) REVERT: A 1181 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 1273 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7243 (mp0) REVERT: A 1385 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7716 (mmtt) REVERT: B 482 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8180 (mmt) REVERT: E 371 MET cc_start: 0.8049 (mtm) cc_final: 0.7784 (mmm) outliers start: 19 outliers final: 12 residues processed: 312 average time/residue: 0.7097 time to fit residues: 237.9157 Evaluate side-chains 317 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 301 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 781 LYS Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1036 ASP Chi-restraints excluded: chain A residue 1065 ASP Chi-restraints excluded: chain A residue 1159 VAL Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 482 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 63 optimal weight: 0.0050 chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 70 optimal weight: 0.3980 chunk 80 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 ASN A 771 GLN A 809 GLN A 870 ASN A1110 GLN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.143745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121280 restraints weight = 17774.405| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.90 r_work: 0.3467 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12796 Z= 0.142 Angle : 0.523 7.614 17286 Z= 0.265 Chirality : 0.041 0.182 1978 Planarity : 0.004 0.047 2183 Dihedral : 3.898 20.206 1711 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.57 % Allowed : 18.26 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 1.56 (0.22), residues: 1544 helix: 2.03 (0.18), residues: 885 sheet: 0.82 (0.59), residues: 84 loop : -0.51 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1389 TYR 0.020 0.001 TYR A1108 PHE 0.031 0.001 PHE A 546 TRP 0.012 0.001 TRP A 440 HIS 0.007 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12792) covalent geometry : angle 0.52321 / 0.27 (17285) hydrogen bonds : bond 0.03836 / 2.58 ( 703) hydrogen bonds : angle 3.81541 / 2.74 ( 2037) metal coordination : bond 0.00390 / 0.20 ( 4) metal coordination : angle 1.27841 / 0.67 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6401.56 seconds wall clock time: 109 minutes 29.93 seconds (6569.93 seconds total)