Starting phenix.real_space_refine on Thu Jul 2 15:20:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qrn_53320/07_2026/9qrn_53320.map" } resolution = 3.1 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 5614 2.51 5 N 1476 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 8773 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 45, 'TRANS': 1067} Chain breaks: 7 Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 2, ' ZN': 4} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2789 SG CYS A 669 63.541 44.507 76.015 1.00 16.38 S ATOM 4758 SG CYS A 918 50.687 86.277 11.236 1.00 69.39 S ATOM 4780 SG CYS A 921 51.371 86.111 8.106 1.00 57.80 S ATOM 4942 SG CYS A 943 51.965 89.264 10.228 1.00 55.87 S ATOM 4964 SG CYS A 946 48.948 87.525 8.563 1.00 76.87 S Time building chain proxies: 2.09, per 1000 atoms: 0.24 Number of scatterers: 8842 At special positions: 0 Unit cell: (101.156, 116.204, 119.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 43 16.00 P 3 15.00 Mg 2 11.99 O 1700 8.00 N 1476 7.00 C 5614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 288.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 346 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 344 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A1502 " - pdb=" NE2 HIS A 744 " pdb=" ZN A1503 " pdb="ZN ZN A1503 " - pdb=" ND1 HIS A 619 " pdb="ZN ZN A1503 " - pdb=" SG CYS A 669 " pdb=" ZN A1504 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 918 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 921 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 946 " pdb="ZN ZN A1504 " - pdb=" SG CYS A 943 " Number of angles added : 6 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2062 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 53.9% alpha, 11.4% 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 357 through 369 Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 491 through 503 Processing helix chain 'A' and resid 512 through 527 removed outlier: 3.675A pdb=" N TYR A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 571 through 593 removed outlier: 4.217A pdb=" N ILE A 585 " --> pdb=" O HIS A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.618A pdb=" N ARG A 614 " --> pdb=" O ASP A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 672 through 681 Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 704 through 710 removed outlier: 3.835A pdb=" N ILE A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 760 through 770 removed outlier: 6.328A pdb=" N GLY A 763 " --> pdb=" O SER A 760 " (cutoff:3.500A) Proline residue: A 766 - end of helix Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.506A pdb=" N CYS A 810 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 Processing helix chain 'A' and resid 849 through 866 Processing helix chain 'A' and resid 868 through 886 removed outlier: 3.518A pdb=" N TYR A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 897 Processing helix chain 'A' and resid 898 through 904 Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 959 through 964 Processing helix chain 'A' and resid 965 through 968 removed outlier: 4.081A pdb=" N ASP A 968 " --> pdb=" O PHE A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 981 through 994 Processing helix chain 'A' and resid 1008 through 1023 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1070 through 1074 Processing helix chain 'A' and resid 1085 through 1090 Processing helix chain 'A' and resid 1102 through 1115 Processing helix chain 'A' and resid 1127 through 1134 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1159 through 1170 Processing helix chain 'A' and resid 1173 through 1185 Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1211 through 1222 Processing helix chain 'A' and resid 1225 through 1238 Processing helix chain 'A' and resid 1245 through 1259 Processing helix chain 'A' and resid 1262 through 1271 removed outlier: 3.839A pdb=" N ILE A1266 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1298 Processing helix chain 'A' and resid 1298 through 1311 Processing helix chain 'A' and resid 1315 through 1322 removed outlier: 3.672A pdb=" N GLY A1322 " --> pdb=" O SER A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1336 removed outlier: 3.770A pdb=" N VAL A1326 " --> pdb=" O GLY A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1360 Processing helix chain 'A' and resid 1387 through 1391 Processing helix chain 'A' and resid 1396 through 1405 Processing helix chain 'A' and resid 1414 through 1422 Processing helix chain 'A' and resid 1425 through 1435 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 378 removed outlier: 6.543A pdb=" N ILE A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY A 401 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE A 375 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A 403 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP A 377 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN A 405 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ILE A 651 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN A 405 " --> pdb=" O ILE A 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 378 removed outlier: 6.543A pdb=" N ILE A 373 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY A 401 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE A 375 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU A 403 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP A 377 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN A 405 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A 400 " --> pdb=" O ALA A 624 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 456 through 464 removed outlier: 6.587A pdb=" N LYS A 451 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER A 460 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 449 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASP A 462 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 447 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE A 464 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 445 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 426 " --> pdb=" O ILE A 507 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL A 509 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 428 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 695 through 698 Processing sheet with id=AA6, first strand: chain 'A' and resid 890 through 892 removed outlier: 3.907A pdb=" N ASP A 974 " --> pdb=" O ARG A 892 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1094 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY A1051 " --> pdb=" O ILE A1098 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY A1100 " --> pdb=" O HIS A1049 " (cutoff:3.500A) removed outlier: 12.684A pdb=" N HIS A1049 " --> pdb=" O GLY A1100 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA A1001 " --> pdb=" O HIS A1049 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N GLY A1051 " --> pdb=" O TYR A 999 " (cutoff:3.500A) removed outlier: 10.107A pdb=" N TYR A 999 " --> pdb=" O GLY A1051 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 924 through 926 Processing sheet with id=AA8, first strand: chain 'A' and resid 1068 through 1069 Processing sheet with id=AA9, first strand: chain 'A' and resid 1363 through 1364 removed outlier: 7.568A pdb=" N LYS A1363 " --> pdb=" O LEU A1384 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1521 1.31 - 1.43: 2341 1.43 - 1.56: 5085 1.56 - 1.69: 5 1.69 - 1.82: 76 Bond restraints: 9028 Sorted by residual: bond pdb=" C GLY A1115 " pdb=" N ILE A1116 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.23e-02 6.61e+03 8.95e+01 bond pdb=" C LEU A1110 " pdb=" N GLN A1111 " ideal model delta sigma weight residual 1.334 1.448 -0.114 1.33e-02 5.65e+03 7.30e+01 bond pdb=" C PHE A 430 " pdb=" N ALA A 431 " ideal model delta sigma weight residual 1.330 1.435 -0.105 1.26e-02 6.30e+03 6.97e+01 bond pdb=" C LYS A 561 " pdb=" N PHE A 562 " ideal model delta sigma weight residual 1.333 1.221 0.112 1.36e-02 5.41e+03 6.73e+01 bond pdb=" C TYR A 704 " pdb=" N ALA A 705 " ideal model delta sigma weight residual 1.332 1.434 -0.102 1.33e-02 5.65e+03 5.93e+01 ... (remaining 9023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 10291 1.93 - 3.87: 1705 3.87 - 5.80: 196 5.80 - 7.73: 20 7.73 - 9.67: 7 Bond angle restraints: 12219 Sorted by residual: angle pdb=" N HIS A1221 " pdb=" CA HIS A1221 " pdb=" C HIS A1221 " ideal model delta sigma weight residual 111.28 103.38 7.90 1.09e+00 8.42e-01 5.25e+01 angle pdb=" N ARG A 647 " pdb=" CA ARG A 647 " pdb=" C ARG A 647 " ideal model delta sigma weight residual 112.88 104.09 8.79 1.29e+00 6.01e-01 4.65e+01 angle pdb=" C ILE A 752 " pdb=" N TYR A 753 " pdb=" CA TYR A 753 " ideal model delta sigma weight residual 120.54 111.47 9.07 1.35e+00 5.49e-01 4.51e+01 angle pdb=" N ARG A1044 " pdb=" CA ARG A1044 " pdb=" C ARG A1044 " ideal model delta sigma weight residual 114.04 106.20 7.84 1.24e+00 6.50e-01 4.00e+01 angle pdb=" N ASP A1315 " pdb=" CA ASP A1315 " pdb=" C ASP A1315 " ideal model delta sigma weight residual 109.39 99.72 9.67 1.59e+00 3.96e-01 3.70e+01 ... (remaining 12214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4501 17.95 - 35.90: 537 35.90 - 53.86: 266 53.86 - 71.81: 80 71.81 - 89.76: 16 Dihedral angle restraints: 5400 sinusoidal: 2180 harmonic: 3220 Sorted by residual: dihedral pdb=" CA THR A1066 " pdb=" C THR A1066 " pdb=" N PRO A1067 " pdb=" CA PRO A1067 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN A 759 " pdb=" CB ASN A 759 " pdb=" CG ASN A 759 " pdb=" OD1 ASN A 759 " ideal model delta sinusoidal sigma weight residual -90.00 -163.30 73.30 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA HIS A 511 " pdb=" C HIS A 511 " pdb=" N ASN A 512 " pdb=" CA ASN A 512 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 5397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1141 0.128 - 0.256: 200 0.256 - 0.384: 2 0.384 - 0.512: 1 0.512 - 0.640: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" P DT E 1 " pdb=" OP1 DT E 1 " pdb=" OP2 DT E 1 " pdb=" O5' DT E 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DA E 2 " pdb=" OP1 DA E 2 " pdb=" OP2 DA E 2 " pdb=" O5' DA E 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA ILE A 871 " pdb=" N ILE A 871 " pdb=" C ILE A 871 " pdb=" CB ILE A 871 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1342 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 758 " -0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C ILE A 758 " 0.086 2.00e-02 2.50e+03 pdb=" O ILE A 758 " -0.032 2.00e-02 2.50e+03 pdb=" N ASN A 759 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 778 " 0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ARG A 778 " -0.074 2.00e-02 2.50e+03 pdb=" O ARG A 778 " 0.027 2.00e-02 2.50e+03 pdb=" N THR A 779 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 921 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C CYS A 921 " -0.070 2.00e-02 2.50e+03 pdb=" O CYS A 921 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN A 922 " 0.024 2.00e-02 2.50e+03 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.26: 6 2.26 - 2.92: 4139 2.92 - 3.58: 13170 3.58 - 4.24: 22038 4.24 - 4.90: 36801 Nonbonded interactions: 76154 Sorted by model distance: nonbonded pdb=" OD2 ASP A1097 " pdb="MG MG A1506 " model vdw 1.595 2.170 nonbonded pdb=" OD2 ASP A 353 " pdb="ZN ZN A1502 " model vdw 1.803 2.230 nonbonded pdb=" OD1 ASN A 742 " pdb="ZN ZN A1501 " model vdw 1.831 2.230 nonbonded pdb=" OE2 GLU A 403 " pdb="ZN ZN A1503 " model vdw 1.886 2.230 nonbonded pdb=" OD1 ASP A 972 " pdb="MG MG A1506 " model vdw 2.182 2.170 ... (remaining 76149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.014 0.552 9038 Z= 0.850 Angle : 1.414 26.832 12225 Z= 1.072 Chirality : 0.091 0.640 1345 Planarity : 0.007 0.050 1575 Dihedral : 20.393 89.759 3338 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 17.92 % Allowed : 20.04 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1097 helix: 0.59 (0.22), residues: 519 sheet: -0.83 (0.68), residues: 53 loop : -0.83 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.023 0.002 TYR A 693 PHE 0.017 0.002 PHE A1230 TRP 0.012 0.002 TRP A1264 HIS 0.009 0.001 HIS A1101 Details of bonding type rmsd/Z covalent geometry : bond 0.01070 / 0.80 ( 9028) covalent geometry : angle 1.38215 / 1.07 (12219) hydrogen bonds : bond 0.16511 / 10.55 ( 431) hydrogen bonds : angle 7.49991 / 5.28 ( 1218) metal coordination : bond 0.25697 / 15.07 ( 10) metal coordination : angle 13.47314 / 7.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 231 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 419 HIS cc_start: 0.7022 (t70) cc_final: 0.6804 (t-170) REVERT: A 481 ILE cc_start: 0.8132 (mt) cc_final: 0.7900 (mt) REVERT: A 546 LEU cc_start: 0.7689 (mt) cc_final: 0.7393 (mt) REVERT: A 562 PHE cc_start: 0.6956 (m-80) cc_final: 0.6610 (m-80) REVERT: A 721 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7641 (tt0) REVERT: A 753 TYR cc_start: 0.7859 (m-10) cc_final: 0.7512 (m-10) REVERT: A 783 MET cc_start: 0.8336 (mmt) cc_final: 0.7793 (mmt) REVERT: A 808 ASP cc_start: 0.7570 (m-30) cc_final: 0.7226 (m-30) REVERT: A 888 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 1010 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7902 (tptt) REVERT: A 1024 ASN cc_start: 0.7259 (t0) cc_final: 0.7008 (t0) REVERT: A 1141 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7534 (m) REVERT: A 1212 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.6261 (ptp-170) REVERT: A 1233 MET cc_start: 0.8461 (ttp) cc_final: 0.8150 (ttp) REVERT: A 1234 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7247 (mm-30) REVERT: A 1422 LYS cc_start: 0.5585 (OUTLIER) cc_final: 0.5192 (mttp) outliers start: 169 outliers final: 51 residues processed: 345 average time/residue: 0.1144 time to fit residues: 52.0218 Evaluate side-chains 197 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 138 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1048 GLN Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1188 ASP Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1221 HIS Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1234 GLU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1275 MET Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1345 LYS Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1415 GLU Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 HIS A 595 ASN A 599 HIS A 605 HIS A 641 ASN A 680 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 922 GLN A 986 HIS A1048 GLN A1119 GLN A1142 GLN A1144 GLN A1179 GLN A1240 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104860 restraints weight = 13358.460| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.02 r_work: 0.3216 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.781 9038 Z= 0.317 Angle : 0.620 10.313 12225 Z= 0.332 Chirality : 0.043 0.184 1345 Planarity : 0.005 0.040 1575 Dihedral : 11.775 69.439 1362 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.36 % Allowed : 21.42 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1097 helix: 1.29 (0.22), residues: 536 sheet: -0.60 (0.51), residues: 90 loop : -0.15 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 571 TYR 0.022 0.002 TYR A 844 PHE 0.017 0.002 PHE A1027 TRP 0.004 0.001 TRP A 368 HIS 0.004 0.001 HIS A 744 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 9028) covalent geometry : angle 0.60359 / 0.33 (12219) hydrogen bonds : bond 0.05331 / 3.53 ( 431) hydrogen bonds : angle 5.73595 / 4.07 ( 1218) metal coordination : bond 0.24732 / 13.03 ( 10) metal coordination : angle 6.50010 / 4.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 150 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 375 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8600 (tp) REVERT: A 463 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6443 (mp0) REVERT: A 485 MET cc_start: 0.6946 (tpp) cc_final: 0.6613 (ttm) REVERT: A 502 PHE cc_start: 0.7404 (t80) cc_final: 0.7196 (t80) REVERT: A 566 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6159 (tp) REVERT: A 647 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6349 (mtm180) REVERT: A 753 TYR cc_start: 0.8398 (m-10) cc_final: 0.7975 (m-80) REVERT: A 783 MET cc_start: 0.8731 (mmt) cc_final: 0.8013 (mmt) REVERT: A 808 ASP cc_start: 0.7861 (m-30) cc_final: 0.7592 (m-30) REVERT: A 1010 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7803 (tptt) REVERT: A 1024 ASN cc_start: 0.7746 (t0) cc_final: 0.7342 (t0) REVERT: A 1028 ARG cc_start: 0.7023 (tpt170) cc_final: 0.6628 (mmp80) REVERT: A 1214 ASP cc_start: 0.7588 (m-30) cc_final: 0.7358 (m-30) REVERT: A 1287 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7933 (tpt) REVERT: A 1422 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5855 (mttp) outliers start: 60 outliers final: 38 residues processed: 195 average time/residue: 0.0918 time to fit residues: 25.2764 Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 750 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1095 LYS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1188 ASP Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1212 ARG Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.103878 restraints weight = 13016.921| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.92 r_work: 0.3202 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9038 Z= 0.137 Angle : 0.541 8.927 12225 Z= 0.292 Chirality : 0.043 0.165 1345 Planarity : 0.004 0.039 1575 Dihedral : 10.002 66.261 1308 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.67 % Allowed : 20.57 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1097 helix: 1.50 (0.22), residues: 543 sheet: -0.59 (0.51), residues: 96 loop : 0.12 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 571 TYR 0.011 0.001 TYR A 916 PHE 0.018 0.002 PHE A 461 TRP 0.003 0.001 TRP A1264 HIS 0.010 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9028) covalent geometry : angle 0.52906 / 0.29 (12219) hydrogen bonds : bond 0.04550 / 3.03 ( 431) hydrogen bonds : angle 5.23671 / 3.68 ( 1218) metal coordination : bond 0.01364 / 0.64 ( 10) metal coordination : angle 5.03649 / 3.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 HIS cc_start: 0.7510 (t70) cc_final: 0.7199 (t-170) REVERT: A 464 PHE cc_start: 0.7458 (m-80) cc_final: 0.7010 (m-80) REVERT: A 485 MET cc_start: 0.7074 (tpp) cc_final: 0.6638 (ttm) REVERT: A 679 MET cc_start: 0.8881 (ttp) cc_final: 0.8599 (ttp) REVERT: A 783 MET cc_start: 0.8889 (mmt) cc_final: 0.8160 (mmt) REVERT: A 808 ASP cc_start: 0.7873 (m-30) cc_final: 0.7563 (m-30) REVERT: A 1010 LYS cc_start: 0.8310 (mttt) cc_final: 0.7910 (tptt) REVERT: A 1024 ASN cc_start: 0.7704 (t0) cc_final: 0.7296 (t0) REVERT: A 1028 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6328 (mmm-85) REVERT: A 1214 ASP cc_start: 0.7479 (m-30) cc_final: 0.7275 (m-30) REVERT: A 1287 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7951 (tpt) REVERT: A 1422 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5790 (mttp) outliers start: 44 outliers final: 30 residues processed: 173 average time/residue: 0.0904 time to fit residues: 22.3547 Evaluate side-chains 160 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN A 955 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098637 restraints weight = 13348.837| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.02 r_work: 0.3116 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9038 Z= 0.162 Angle : 0.531 8.456 12225 Z= 0.288 Chirality : 0.043 0.184 1345 Planarity : 0.004 0.042 1575 Dihedral : 8.897 64.743 1271 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.35 % Allowed : 21.85 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1097 helix: 1.55 (0.22), residues: 542 sheet: -0.62 (0.51), residues: 96 loop : 0.10 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 614 TYR 0.011 0.002 TYR A 453 PHE 0.012 0.002 PHE A 461 TRP 0.003 0.001 TRP A1079 HIS 0.007 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9028) covalent geometry : angle 0.52059 / 0.29 (12219) hydrogen bonds : bond 0.04534 / 3.04 ( 431) hydrogen bonds : angle 5.14713 / 3.61 ( 1218) metal coordination : bond 0.00711 / 0.35 ( 10) metal coordination : angle 4.68130 / 2.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.414 Fit side-chains REVERT: A 464 PHE cc_start: 0.7622 (m-80) cc_final: 0.7113 (m-80) REVERT: A 478 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7715 (tm) REVERT: A 485 MET cc_start: 0.7343 (tpp) cc_final: 0.6802 (ttm) REVERT: A 688 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.8014 (t0) REVERT: A 783 MET cc_start: 0.8858 (mmt) cc_final: 0.8099 (mmt) REVERT: A 808 ASP cc_start: 0.7938 (m-30) cc_final: 0.7584 (m-30) REVERT: A 949 ARG cc_start: 0.7460 (ttp-170) cc_final: 0.7069 (ptt-90) REVERT: A 1010 LYS cc_start: 0.8377 (mttt) cc_final: 0.7910 (tptt) REVERT: A 1024 ASN cc_start: 0.7796 (t0) cc_final: 0.7366 (t0) REVERT: A 1028 ARG cc_start: 0.7110 (tpm170) cc_final: 0.6317 (mmm-85) REVERT: A 1287 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8067 (tpt) REVERT: A 1422 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5807 (mttt) REVERT: A 1431 MET cc_start: 0.8377 (mtt) cc_final: 0.8134 (mtp) outliers start: 41 outliers final: 31 residues processed: 168 average time/residue: 0.0803 time to fit residues: 19.8321 Evaluate side-chains 158 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1094 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099953 restraints weight = 13202.386| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.99 r_work: 0.3129 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9038 Z= 0.125 Angle : 0.491 7.677 12225 Z= 0.264 Chirality : 0.041 0.145 1345 Planarity : 0.004 0.041 1575 Dihedral : 8.736 65.196 1271 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.71 % Allowed : 22.69 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1097 helix: 1.69 (0.22), residues: 542 sheet: -0.47 (0.52), residues: 96 loop : 0.20 (0.32), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.009 0.001 TYR A 916 PHE 0.020 0.001 PHE A 461 TRP 0.003 0.001 TRP A1079 HIS 0.006 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9028) covalent geometry : angle 0.48258 / 0.26 (12219) hydrogen bonds : bond 0.04112 / 2.75 ( 431) hydrogen bonds : angle 4.97292 / 3.49 ( 1218) metal coordination : bond 0.00374 / 0.17 ( 10) metal coordination : angle 4.14883 / 2.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.427 Fit side-chains REVERT: A 454 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7178 (tppt) REVERT: A 464 PHE cc_start: 0.7470 (m-80) cc_final: 0.6660 (m-80) REVERT: A 478 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7718 (tm) REVERT: A 485 MET cc_start: 0.7436 (tpp) cc_final: 0.6858 (ttm) REVERT: A 688 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (t0) REVERT: A 783 MET cc_start: 0.8858 (mmt) cc_final: 0.8124 (mmt) REVERT: A 808 ASP cc_start: 0.7978 (m-30) cc_final: 0.7649 (m-30) REVERT: A 949 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7197 (ptt-90) REVERT: A 1010 LYS cc_start: 0.8427 (mttt) cc_final: 0.7936 (tptt) REVERT: A 1024 ASN cc_start: 0.7803 (t0) cc_final: 0.7401 (t0) REVERT: A 1028 ARG cc_start: 0.7076 (tpm170) cc_final: 0.6252 (mmm-85) REVERT: A 1214 ASP cc_start: 0.7525 (m-30) cc_final: 0.7258 (m-30) REVERT: A 1287 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8068 (tpt) REVERT: A 1422 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5817 (ttmt) REVERT: A 1431 MET cc_start: 0.8279 (mtt) cc_final: 0.8045 (mtp) outliers start: 35 outliers final: 25 residues processed: 157 average time/residue: 0.0828 time to fit residues: 18.7466 Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 688 ASN Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS A 853 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.093762 restraints weight = 13483.883| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.04 r_work: 0.3032 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9038 Z= 0.272 Angle : 0.630 8.717 12225 Z= 0.339 Chirality : 0.046 0.147 1345 Planarity : 0.005 0.037 1575 Dihedral : 8.856 63.040 1267 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.56 % Allowed : 23.22 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1097 helix: 1.17 (0.21), residues: 542 sheet: -0.95 (0.46), residues: 105 loop : -0.06 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 614 TYR 0.017 0.002 TYR A1070 PHE 0.030 0.003 PHE A1161 TRP 0.007 0.002 TRP A 368 HIS 0.010 0.002 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 ( 9028) covalent geometry : angle 0.62234 / 0.34 (12219) hydrogen bonds : bond 0.05228 / 3.58 ( 431) hydrogen bonds : angle 5.28742 / 3.69 ( 1218) metal coordination : bond 0.00699 / 0.33 ( 10) metal coordination : angle 4.42242 / 2.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 464 PHE cc_start: 0.7742 (m-80) cc_final: 0.7190 (m-80) REVERT: A 485 MET cc_start: 0.7508 (tpp) cc_final: 0.6999 (ttm) REVERT: A 685 GLU cc_start: 0.7566 (tp30) cc_final: 0.7238 (tp30) REVERT: A 808 ASP cc_start: 0.8027 (m-30) cc_final: 0.7758 (m-30) REVERT: A 1010 LYS cc_start: 0.8440 (mttt) cc_final: 0.7820 (tptt) REVERT: A 1024 ASN cc_start: 0.7771 (t0) cc_final: 0.7349 (t0) REVERT: A 1214 ASP cc_start: 0.7635 (m-30) cc_final: 0.7373 (m-30) REVERT: A 1287 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8074 (tpt) REVERT: A 1422 LYS cc_start: 0.6165 (OUTLIER) cc_final: 0.5655 (ttmt) REVERT: A 1431 MET cc_start: 0.8360 (mtt) cc_final: 0.8159 (mtp) outliers start: 43 outliers final: 30 residues processed: 157 average time/residue: 0.0856 time to fit residues: 19.4622 Evaluate side-chains 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.096589 restraints weight = 13335.675| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.03 r_work: 0.3077 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9038 Z= 0.128 Angle : 0.517 7.003 12225 Z= 0.277 Chirality : 0.042 0.140 1345 Planarity : 0.004 0.037 1575 Dihedral : 8.652 64.770 1265 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.50 % Allowed : 24.39 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1097 helix: 1.52 (0.22), residues: 541 sheet: -0.67 (0.47), residues: 101 loop : 0.02 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 614 TYR 0.012 0.001 TYR A 916 PHE 0.023 0.002 PHE A1161 TRP 0.004 0.001 TRP A 584 HIS 0.005 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9028) covalent geometry : angle 0.51053 / 0.28 (12219) hydrogen bonds : bond 0.04275 / 2.89 ( 431) hydrogen bonds : angle 5.03146 / 3.53 ( 1218) metal coordination : bond 0.00297 / 0.14 ( 10) metal coordination : angle 3.72884 / 2.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.345 Fit side-chains REVERT: A 434 THR cc_start: 0.8969 (m) cc_final: 0.8684 (p) REVERT: A 464 PHE cc_start: 0.7629 (m-80) cc_final: 0.7102 (m-80) REVERT: A 485 MET cc_start: 0.7529 (tpp) cc_final: 0.7027 (ttm) REVERT: A 808 ASP cc_start: 0.8001 (m-30) cc_final: 0.7725 (m-30) REVERT: A 920 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: A 1010 LYS cc_start: 0.8471 (mttt) cc_final: 0.7878 (tptt) REVERT: A 1024 ASN cc_start: 0.7772 (t0) cc_final: 0.7353 (t0) REVERT: A 1129 MET cc_start: 0.8068 (mmm) cc_final: 0.4990 (ptp) REVERT: A 1214 ASP cc_start: 0.7687 (m-30) cc_final: 0.7372 (m-30) REVERT: A 1287 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8029 (tpt) REVERT: A 1422 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5659 (ttmt) REVERT: A 1431 MET cc_start: 0.8314 (mtt) cc_final: 0.8096 (mtp) outliers start: 33 outliers final: 27 residues processed: 156 average time/residue: 0.0897 time to fit residues: 20.3412 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1324 ASP Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.124101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098182 restraints weight = 13193.693| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.01 r_work: 0.3102 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9038 Z= 0.111 Angle : 0.491 6.725 12225 Z= 0.262 Chirality : 0.041 0.139 1345 Planarity : 0.004 0.034 1575 Dihedral : 8.439 66.461 1265 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.61 % Allowed : 24.39 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.26), residues: 1097 helix: 1.69 (0.22), residues: 540 sheet: -0.42 (0.55), residues: 72 loop : 0.03 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.012 0.001 TYR A 441 PHE 0.021 0.001 PHE A1161 TRP 0.004 0.001 TRP A 584 HIS 0.004 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9028) covalent geometry : angle 0.48558 / 0.26 (12219) hydrogen bonds : bond 0.03956 / 2.66 ( 431) hydrogen bonds : angle 4.85959 / 3.41 ( 1218) metal coordination : bond 0.00227 / 0.10 ( 10) metal coordination : angle 3.40837 / 2.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 434 THR cc_start: 0.8886 (m) cc_final: 0.8661 (p) REVERT: A 464 PHE cc_start: 0.7536 (m-80) cc_final: 0.7038 (m-80) REVERT: A 485 MET cc_start: 0.7567 (tpp) cc_final: 0.7092 (ttm) REVERT: A 790 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8554 (mp) REVERT: A 808 ASP cc_start: 0.8003 (m-30) cc_final: 0.7731 (m-30) REVERT: A 920 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: A 1010 LYS cc_start: 0.8442 (mttt) cc_final: 0.7856 (tptt) REVERT: A 1024 ASN cc_start: 0.7738 (t0) cc_final: 0.7325 (t0) REVERT: A 1129 MET cc_start: 0.8013 (mmm) cc_final: 0.5026 (ptp) REVERT: A 1188 ASP cc_start: 0.8024 (t0) cc_final: 0.7824 (t0) REVERT: A 1287 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8071 (tpt) REVERT: A 1380 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7867 (pt0) REVERT: A 1422 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5732 (ttmt) REVERT: A 1431 MET cc_start: 0.8287 (mtt) cc_final: 0.8072 (mtp) outliers start: 34 outliers final: 24 residues processed: 155 average time/residue: 0.0898 time to fit residues: 20.1548 Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096427 restraints weight = 13339.389| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.03 r_work: 0.3073 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9038 Z= 0.149 Angle : 0.517 7.214 12225 Z= 0.276 Chirality : 0.042 0.136 1345 Planarity : 0.004 0.036 1575 Dihedral : 8.331 65.502 1261 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.97 % Allowed : 25.03 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1097 helix: 1.64 (0.22), residues: 543 sheet: -0.45 (0.48), residues: 91 loop : -0.05 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 614 TYR 0.017 0.001 TYR A 453 PHE 0.019 0.002 PHE A 461 TRP 0.004 0.001 TRP A1264 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9028) covalent geometry : angle 0.51192 / 0.28 (12219) hydrogen bonds : bond 0.04224 / 2.88 ( 431) hydrogen bonds : angle 4.91376 / 3.43 ( 1218) metal coordination : bond 0.00376 / 0.17 ( 10) metal coordination : angle 3.42324 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 434 THR cc_start: 0.8896 (m) cc_final: 0.8664 (p) REVERT: A 464 PHE cc_start: 0.7631 (m-80) cc_final: 0.7133 (m-80) REVERT: A 485 MET cc_start: 0.7607 (tpp) cc_final: 0.7130 (ttm) REVERT: A 808 ASP cc_start: 0.8004 (m-30) cc_final: 0.7746 (m-30) REVERT: A 920 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: A 1010 LYS cc_start: 0.8454 (mttt) cc_final: 0.7812 (tptt) REVERT: A 1024 ASN cc_start: 0.7754 (t0) cc_final: 0.7339 (t0) REVERT: A 1188 ASP cc_start: 0.8004 (t0) cc_final: 0.7791 (t0) REVERT: A 1214 ASP cc_start: 0.7497 (m-30) cc_final: 0.7285 (m-30) REVERT: A 1287 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8088 (tpt) REVERT: A 1380 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7808 (pt0) REVERT: A 1422 LYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5626 (ttmt) REVERT: A 1431 MET cc_start: 0.8290 (mtt) cc_final: 0.8081 (mtp) outliers start: 28 outliers final: 23 residues processed: 151 average time/residue: 0.0898 time to fit residues: 19.5347 Evaluate side-chains 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 790 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1422 LYS Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098014 restraints weight = 13287.251| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.03 r_work: 0.3099 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9038 Z= 0.113 Angle : 0.499 8.948 12225 Z= 0.267 Chirality : 0.041 0.134 1345 Planarity : 0.004 0.035 1575 Dihedral : 8.201 66.344 1260 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 25.45 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1097 helix: 1.74 (0.22), residues: 543 sheet: -0.30 (0.55), residues: 72 loop : 0.01 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 473 TYR 0.012 0.001 TYR A 916 PHE 0.020 0.001 PHE A 461 TRP 0.004 0.001 TRP A 584 HIS 0.004 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 9028) covalent geometry : angle 0.49394 / 0.27 (12219) hydrogen bonds : bond 0.03958 / 2.66 ( 431) hydrogen bonds : angle 4.85143 / 3.39 ( 1218) metal coordination : bond 0.00207 / 0.10 ( 10) metal coordination : angle 3.22177 / 1.93 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 464 PHE cc_start: 0.7609 (m-80) cc_final: 0.7128 (m-80) REVERT: A 485 MET cc_start: 0.7610 (tpp) cc_final: 0.7172 (ttm) REVERT: A 785 THR cc_start: 0.8840 (m) cc_final: 0.8527 (p) REVERT: A 808 ASP cc_start: 0.8006 (m-30) cc_final: 0.7735 (m-30) REVERT: A 1010 LYS cc_start: 0.8427 (mttt) cc_final: 0.7816 (tptt) REVERT: A 1024 ASN cc_start: 0.7742 (t0) cc_final: 0.7339 (t0) REVERT: A 1129 MET cc_start: 0.8131 (mmm) cc_final: 0.5103 (ptp) REVERT: A 1188 ASP cc_start: 0.7973 (t0) cc_final: 0.7086 (t0) REVERT: A 1214 ASP cc_start: 0.7438 (m-30) cc_final: 0.7215 (m-30) REVERT: A 1287 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8101 (tpt) REVERT: A 1380 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7832 (pt0) REVERT: A 1431 MET cc_start: 0.8282 (mtt) cc_final: 0.8072 (mtp) outliers start: 25 outliers final: 22 residues processed: 146 average time/residue: 0.0877 time to fit residues: 18.6349 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 924 SER Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1090 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1159 THR Chi-restraints excluded: chain A residue 1213 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1286 LEU Chi-restraints excluded: chain A residue 1287 MET Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain A residue 1437 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 106 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098663 restraints weight = 13283.516| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.93 r_work: 0.3107 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9038 Z= 0.122 Angle : 0.500 7.645 12225 Z= 0.267 Chirality : 0.041 0.138 1345 Planarity : 0.004 0.035 1575 Dihedral : 7.796 66.427 1254 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.76 % Allowed : 25.77 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1097 helix: 1.75 (0.22), residues: 543 sheet: -0.21 (0.56), residues: 72 loop : -0.02 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.013 0.001 TYR A 453 PHE 0.019 0.001 PHE A 461 TRP 0.005 0.001 TRP A 584 HIS 0.004 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9028) covalent geometry : angle 0.49551 / 0.27 (12219) hydrogen bonds : bond 0.03973 / 2.69 ( 431) hydrogen bonds : angle 4.84558 / 3.38 ( 1218) metal coordination : bond 0.00278 / 0.12 ( 10) metal coordination : angle 3.05532 / 1.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.34 seconds wall clock time: 44 minutes 57.66 seconds (2697.66 seconds total)