Starting phenix.real_space_refine on Tue Aug 26 00:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a22_6337/08_2025/5a22_6337.map" } resolution = 3.8 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= 0.052 sd= 0.385 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 89 5.16 5 C 10249 2.51 5 N 2803 2.21 5 O 2934 1.98 5 H 16110 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32187 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 32185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2002, 32185 Classifications: {'peptide': 2002} Link IDs: {'PTRANS': 93, 'TRANS': 1908} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17047 SG CYS A1081 70.220 68.005 80.519 1.00193.79 S ATOM 20418 SG CYS A1299 67.983 67.609 80.307 1.00220.85 S ATOM 20461 SG CYS A1302 67.501 70.395 78.910 1.00140.37 S ATOM 17656 SG CYS A1120 68.106 51.296 71.661 1.00172.55 S ATOM 17690 SG CYS A1123 67.624 52.782 73.640 1.00217.61 S Time building chain proxies: 4.42, per 1000 atoms: 0.14 Number of scatterers: 32187 At special positions: 0 Unit cell: (123.7, 134.833, 98.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 89 16.00 O 2934 8.00 N 2803 7.00 C 10249 6.00 H 16110 1.00 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: 2.29 Conformation dependent library (CDL) restraints added in 787.4 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1302 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1299 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1081 " pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1294 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1296 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1120 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1123 " Number of angles added : 2 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 8 sheets defined 55.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.949A pdb=" N SER A 68 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 106 through 135 removed outlier: 3.534A pdb=" N TYR A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 228 through 250 removed outlier: 4.601A pdb=" N CYS A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 304 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 311 through 329 removed outlier: 4.341A pdb=" N GLU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.815A pdb=" N THR A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 384 through 406 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 460 through 464 removed outlier: 4.126A pdb=" N ILE A 463 " --> pdb=" O ASP A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 519 through 522 Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 564 through 567 Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 614 through 629 Proline residue: A 620 - end of helix Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 645 Processing helix chain 'A' and resid 652 through 656 removed outlier: 3.818A pdb=" N LEU A 655 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 700 Processing helix chain 'A' and resid 730 through 758 removed outlier: 3.596A pdb=" N GLN A 734 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 807 through 826 removed outlier: 4.007A pdb=" N MET A 812 " --> pdb=" O CYS A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 850 Processing helix chain 'A' and resid 870 through 880 Processing helix chain 'A' and resid 902 through 918 Processing helix chain 'A' and resid 921 through 932 Processing helix chain 'A' and resid 939 through 949 Processing helix chain 'A' and resid 960 through 976 Processing helix chain 'A' and resid 982 through 1005 removed outlier: 6.194A pdb=" N ASP A 997 " --> pdb=" O TYR A 993 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1021 Processing helix chain 'A' and resid 1023 through 1033 removed outlier: 3.689A pdb=" N PHE A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1043 through 1045 No H-bonds generated for 'chain 'A' and resid 1043 through 1045' Processing helix chain 'A' and resid 1048 through 1070 removed outlier: 4.106A pdb=" N ASP A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 removed outlier: 4.152A pdb=" N HIS A1085 " --> pdb=" O CYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 3.863A pdb=" N MET A1109 " --> pdb=" O HIS A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1186 Processing helix chain 'A' and resid 1195 through 1209 Processing helix chain 'A' and resid 1243 through 1250 removed outlier: 4.057A pdb=" N LEU A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1285 Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 3.871A pdb=" N ASN A1331 " --> pdb=" O LYS A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1377 Processing helix chain 'A' and resid 1397 through 1420 Processing helix chain 'A' and resid 1427 through 1446 Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 3.644A pdb=" N LEU A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.722A pdb=" N GLU A1461 " --> pdb=" O PRO A1457 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE A1465 " --> pdb=" O GLU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1498 Processing helix chain 'A' and resid 1515 through 1533 removed outlier: 4.606A pdb=" N ILE A1519 " --> pdb=" O SER A1515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A1520 " --> pdb=" O ILE A1516 " (cutoff:3.500A) Proline residue: A1521 - end of helix Processing helix chain 'A' and resid 1540 through 1556 removed outlier: 3.755A pdb=" N GLU A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1640 removed outlier: 4.464A pdb=" N SER A1637 " --> pdb=" O ASN A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1659 Processing helix chain 'A' and resid 1674 through 1684 Processing helix chain 'A' and resid 1710 through 1717 removed outlier: 3.663A pdb=" N LEU A1716 " --> pdb=" O LEU A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1732 removed outlier: 3.842A pdb=" N TYR A1732 " --> pdb=" O CYS A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1753 Processing helix chain 'A' and resid 1767 through 1782 Processing helix chain 'A' and resid 1783 through 1785 No H-bonds generated for 'chain 'A' and resid 1783 through 1785' Processing helix chain 'A' and resid 1797 through 1804 removed outlier: 4.186A pdb=" N SER A1804 " --> pdb=" O TYR A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1811 Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1867 through 1881 Processing helix chain 'A' and resid 1896 through 1906 Processing helix chain 'A' and resid 1909 through 1923 Processing helix chain 'A' and resid 1927 through 1944 Processing helix chain 'A' and resid 1958 through 1980 Processing helix chain 'A' and resid 1981 through 1994 removed outlier: 3.795A pdb=" N TYR A1985 " --> pdb=" O ASP A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2045 Processing helix chain 'A' and resid 2053 through 2065 Processing helix chain 'A' and resid 2069 through 2075 Processing helix chain 'A' and resid 2079 through 2083 Processing sheet with id=AA, first strand: chain 'A' and resid 189 through 193 Processing sheet with id=AB, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AC, first strand: chain 'A' and resid 706 through 712 Processing sheet with id=AD, first strand: chain 'A' and resid 657 through 659 Processing sheet with id=AE, first strand: chain 'A' and resid 774 through 776 Processing sheet with id=AF, first strand: chain 'A' and resid 1114 through 1115 Processing sheet with id=AG, first strand: chain 'A' and resid 1608 through 1613 removed outlier: 3.595A pdb=" N THR A1608 " --> pdb=" O VAL A1822 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A1822 " --> pdb=" O THR A1608 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 2012 through 2014 848 hydrogen bonds defined for protein. 2439 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: 6.65 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16083 1.04 - 1.24: 1860 1.24 - 1.44: 5254 1.44 - 1.64: 9223 1.64 - 1.84: 146 Bond restraints: 32566 Sorted by residual: bond pdb=" CA VAL A 289 " pdb=" CB VAL A 289 " ideal model delta sigma weight residual 1.540 1.613 -0.073 1.11e-02 8.12e+03 4.36e+01 bond pdb=" CA ILE A 865 " pdb=" CB ILE A 865 " ideal model delta sigma weight residual 1.537 1.603 -0.065 1.29e-02 6.01e+03 2.58e+01 bond pdb=" C GLN A 721 " pdb=" O GLN A 721 " ideal model delta sigma weight residual 1.235 1.286 -0.051 1.18e-02 7.18e+03 1.89e+01 bond pdb=" CA THR A 817 " pdb=" CB THR A 817 " ideal model delta sigma weight residual 1.529 1.591 -0.062 1.58e-02 4.01e+03 1.54e+01 bond pdb=" C ILE A 122 " pdb=" O ILE A 122 " ideal model delta sigma weight residual 1.236 1.280 -0.043 1.11e-02 8.12e+03 1.52e+01 ... (remaining 32561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 56861 2.46 - 4.93: 1731 4.93 - 7.39: 230 7.39 - 9.85: 35 9.85 - 12.32: 12 Bond angle restraints: 58869 Sorted by residual: angle pdb=" C GLN A1165 " pdb=" N PRO A1166 " pdb=" CA PRO A1166 " ideal model delta sigma weight residual 119.84 107.78 12.06 1.25e+00 6.40e-01 9.31e+01 angle pdb=" N PRO A1447 " pdb=" CA PRO A1447 " pdb=" C PRO A1447 " ideal model delta sigma weight residual 110.70 120.60 -9.90 1.22e+00 6.72e-01 6.59e+01 angle pdb=" C ASN A1954 " pdb=" N PRO A1955 " pdb=" CA PRO A1955 " ideal model delta sigma weight residual 120.38 112.22 8.16 1.03e+00 9.43e-01 6.27e+01 angle pdb=" C ILE A 62 " pdb=" N PRO A 63 " pdb=" CA PRO A 63 " ideal model delta sigma weight residual 119.84 110.49 9.35 1.25e+00 6.40e-01 5.59e+01 angle pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" C ILE A 332 " ideal model delta sigma weight residual 110.62 103.24 7.38 1.02e+00 9.61e-01 5.23e+01 ... (remaining 58864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 13571 18.14 - 36.27: 1083 36.27 - 54.41: 339 54.41 - 72.55: 293 72.55 - 90.68: 12 Dihedral angle restraints: 15298 sinusoidal: 8355 harmonic: 6943 Sorted by residual: dihedral pdb=" CA GLU A 766 " pdb=" C GLU A 766 " pdb=" N THR A 767 " pdb=" CA THR A 767 " ideal model delta harmonic sigma weight residual -180.00 -134.47 -45.53 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA ALA A1151 " pdb=" C ALA A1151 " pdb=" N TYR A1152 " pdb=" CA TYR A1152 " ideal model delta harmonic sigma weight residual 180.00 137.82 42.18 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA TRP A1167 " pdb=" C TRP A1167 " pdb=" N GLU A1168 " pdb=" CA GLU A1168 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 ... (remaining 15295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1945 0.068 - 0.137: 438 0.137 - 0.205: 69 0.205 - 0.274: 7 0.274 - 0.342: 1 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA TYR A 879 " pdb=" N TYR A 879 " pdb=" C TYR A 879 " pdb=" CB TYR A 879 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA HIS A2067 " pdb=" N HIS A2067 " pdb=" C HIS A2067 " pdb=" CB HIS A2067 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE A2083 " pdb=" N ILE A2083 " pdb=" C ILE A2083 " pdb=" CB ILE A2083 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2457 not shown) Planarity restraints: 4734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1955 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO A1956 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO A1956 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1956 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1954 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A1955 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1955 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1955 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 609 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.25e+00 pdb=" C TRP A 609 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP A 609 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 610 " -0.016 2.00e-02 2.50e+03 ... (remaining 4731 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 1296 2.11 - 2.73: 58423 2.73 - 3.35: 96523 3.35 - 3.98: 122110 3.98 - 4.60: 192250 Nonbonded interactions: 470602 Sorted by model distance: nonbonded pdb=" O TRP A2013 " pdb=" HG1 THR A2077 " model vdw 1.482 2.450 nonbonded pdb=" H SER A 471 " pdb=" O MET A 544 " model vdw 1.491 2.450 nonbonded pdb=" O SER A 354 " pdb=" H ARG A 356 " model vdw 1.539 2.450 nonbonded pdb=" O LEU A 629 " pdb=" H TYR A 631 " model vdw 1.546 2.450 nonbonded pdb=" O THR A1254 " pdb=" H MET A1257 " model vdw 1.557 2.450 ... (remaining 470597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.160 Extract box with map and model: 0.330 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 32.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.010 0.273 16463 Z= 0.577 Angle : 1.540 57.168 22272 Z= 0.980 Chirality : 0.058 0.342 2460 Planarity : 0.008 0.100 2828 Dihedral : 15.754 90.682 6145 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 1.96 % Allowed : 13.89 % Favored : 84.15 % Rotamer: Outliers : 5.57 % Allowed : 13.21 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % Twisted General : 0.58 % 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 aren not related in a simple way. whole: -5.08 (0.13), residues: 1994 helix: -3.24 (0.11), residues: 959 sheet: -1.56 (0.41), residues: 113 loop : -3.75 (0.15), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1396 TYR 0.037 0.003 TYR A 879 PHE 0.029 0.003 PHE A1896 TRP 0.022 0.003 TRP A1079 HIS 0.014 0.002 HIS A2067 Details of bonding type rmsd covalent geometry : bond 0.00932 (16456) covalent geometry : angle 1.48976 (22270) hydrogen bonds : bond 0.12572 ( 848) hydrogen bonds : angle 9.01081 ( 2439) metal coordination : bond 0.14565 ( 7) metal coordination : angle 41.22304 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 457 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TRP cc_start: 0.8822 (m-10) cc_final: 0.8613 (m-10) REVERT: A 76 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7958 (mt-10) REVERT: A 113 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 147 TRP cc_start: 0.8732 (m100) cc_final: 0.8439 (m100) REVERT: A 172 ASN cc_start: 0.8536 (t0) cc_final: 0.8023 (t0) REVERT: A 199 ILE cc_start: 0.8815 (mt) cc_final: 0.8446 (pt) REVERT: A 202 ILE cc_start: 0.8708 (tp) cc_final: 0.8196 (tt) REVERT: A 210 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8910 (t) REVERT: A 220 LYS cc_start: 0.8187 (ptmt) cc_final: 0.7945 (tptp) REVERT: A 253 ASP cc_start: 0.8718 (m-30) cc_final: 0.8160 (p0) REVERT: A 288 MET cc_start: 0.8493 (mmp) cc_final: 0.8114 (ttm) REVERT: A 295 LEU cc_start: 0.9267 (tp) cc_final: 0.9020 (tt) REVERT: A 315 GLU cc_start: 0.9057 (tt0) cc_final: 0.8417 (tm-30) REVERT: A 343 LYS cc_start: 0.9322 (mttt) cc_final: 0.9038 (mmtt) REVERT: A 414 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8532 (p0) REVERT: A 422 PHE cc_start: 0.7458 (t80) cc_final: 0.7157 (t80) REVERT: A 442 ASP cc_start: 0.8630 (m-30) cc_final: 0.8382 (m-30) REVERT: A 460 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7607 (p0) REVERT: A 507 LYS cc_start: 0.8616 (tttt) cc_final: 0.8329 (tptt) REVERT: A 512 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8305 (pt0) REVERT: A 521 ASP cc_start: 0.8705 (m-30) cc_final: 0.8295 (t0) REVERT: A 543 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9433 (pt) REVERT: A 547 LYS cc_start: 0.8881 (mttm) cc_final: 0.8652 (mttp) REVERT: A 551 TYR cc_start: 0.9262 (t80) cc_final: 0.8978 (t80) REVERT: A 568 LYS cc_start: 0.8727 (mttm) cc_final: 0.7998 (tttp) REVERT: A 576 LEU cc_start: 0.9017 (tp) cc_final: 0.8686 (tt) REVERT: A 595 TYR cc_start: 0.8735 (m-80) cc_final: 0.7993 (m-80) REVERT: A 722 TYR cc_start: 0.9381 (m-80) cc_final: 0.8976 (m-80) REVERT: A 745 GLU cc_start: 0.8924 (tt0) cc_final: 0.8713 (tp30) REVERT: A 776 TYR cc_start: 0.8739 (t80) cc_final: 0.8430 (t80) REVERT: A 848 MET cc_start: 0.9085 (mmp) cc_final: 0.8734 (mmp) REVERT: A 851 ASP cc_start: 0.8856 (t0) cc_final: 0.8537 (t70) REVERT: A 863 ASP cc_start: 0.8566 (m-30) cc_final: 0.7902 (m-30) REVERT: A 879 TYR cc_start: 0.9310 (m-80) cc_final: 0.9021 (m-80) REVERT: A 968 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8816 (mm-30) REVERT: A 1007 ASN cc_start: 0.8132 (p0) cc_final: 0.7710 (m-40) REVERT: A 1077 LYS cc_start: 0.9074 (mttt) cc_final: 0.8700 (mmtp) REVERT: A 1080 THR cc_start: 0.9213 (m) cc_final: 0.8955 (p) REVERT: A 1137 ASP cc_start: 0.8861 (t0) cc_final: 0.8627 (t0) REVERT: A 1228 ARG cc_start: 0.7135 (ttt180) cc_final: 0.6696 (mmt180) REVERT: A 1241 SER cc_start: 0.9479 (t) cc_final: 0.9105 (p) REVERT: A 1257 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8800 (mtm) REVERT: A 1267 PHE cc_start: 0.8398 (p90) cc_final: 0.8142 (p90) REVERT: A 1287 TRP cc_start: 0.8657 (t-100) cc_final: 0.8456 (t-100) REVERT: A 1308 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8064 (mt-10) REVERT: A 1317 TYR cc_start: 0.7807 (t80) cc_final: 0.6944 (t80) REVERT: A 1384 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7717 (m) REVERT: A 1398 ARG cc_start: 0.8325 (ptt180) cc_final: 0.7890 (mtp180) REVERT: A 1408 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 1427 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7769 (mpp80) REVERT: A 1442 LYS cc_start: 0.8820 (tptt) cc_final: 0.8556 (tttm) REVERT: A 1467 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 1468 LYS cc_start: 0.8801 (tptp) cc_final: 0.8554 (tptt) REVERT: A 1507 LEU cc_start: 0.8961 (mt) cc_final: 0.7581 (pt) REVERT: A 1609 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 1661 ILE cc_start: 0.9167 (mp) cc_final: 0.8636 (mt) REVERT: A 1663 TYR cc_start: 0.9215 (p90) cc_final: 0.8828 (p90) REVERT: A 1668 SER cc_start: 0.9492 (t) cc_final: 0.9190 (t) REVERT: A 1762 ASP cc_start: 0.7884 (m-30) cc_final: 0.7521 (m-30) REVERT: A 1788 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8955 (mp0) REVERT: A 1789 GLN cc_start: 0.8085 (pm20) cc_final: 0.7164 (tm-30) REVERT: A 1794 TYR cc_start: 0.9317 (t80) cc_final: 0.9051 (t80) REVERT: A 1807 ASN cc_start: 0.8927 (m-40) cc_final: 0.8608 (m-40) REVERT: A 1882 PHE cc_start: 0.7971 (m-10) cc_final: 0.7428 (m-10) REVERT: A 1902 MET cc_start: 0.8634 (mtp) cc_final: 0.8264 (mmm) REVERT: A 1918 LEU cc_start: 0.8707 (mt) cc_final: 0.8386 (mm) REVERT: A 1980 LYS cc_start: 0.7497 (mmmt) cc_final: 0.6937 (tptm) REVERT: A 2036 TRP cc_start: 0.9470 (OUTLIER) cc_final: 0.9161 (m100) REVERT: A 2065 ASP cc_start: 0.9163 (m-30) cc_final: 0.8882 (m-30) REVERT: A 2072 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8707 (t0) REVERT: A 2086 ARG cc_start: 0.7858 (ptm-80) cc_final: 0.7490 (ptm-80) REVERT: A 2092 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8102 (ttm-80) outliers start: 100 outliers final: 35 residues processed: 530 average time/residue: 0.2850 time to fit residues: 216.1677 Evaluate side-chains 383 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 336 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1167 TRP Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1476 SER Chi-restraints excluded: chain A residue 1609 ILE Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1761 MET Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2036 TRP Chi-restraints excluded: chain A residue 2071 SER Chi-restraints excluded: chain A residue 2072 ASN Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 159 GLN A 278 GLN A 425 HIS A 618 ASN A 856 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.168679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.145502 restraints weight = 81388.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.152023 restraints weight = 34705.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.156047 restraints weight = 19289.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.158601 restraints weight = 12594.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.160268 restraints weight = 9150.270| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16463 Z= 0.191 Angle : 0.800 16.450 22272 Z= 0.429 Chirality : 0.044 0.201 2460 Planarity : 0.006 0.106 2828 Dihedral : 9.564 70.657 2268 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 1.20 % Allowed : 12.44 % Favored : 86.36 % Rotamer: Outliers : 3.90 % Allowed : 18.23 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % Twisted General : 0.31 % 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 aren not related in a simple way. whole: -3.43 (0.16), residues: 1994 helix: -1.33 (0.14), residues: 996 sheet: -1.86 (0.40), residues: 113 loop : -3.51 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1923 TYR 0.020 0.002 TYR A1375 PHE 0.033 0.002 PHE A 219 TRP 0.026 0.002 TRP A1079 HIS 0.007 0.001 HIS A1105 Details of bonding type rmsd covalent geometry : bond 0.00402 (16456) covalent geometry : angle 0.79051 (22270) hydrogen bonds : bond 0.06404 ( 848) hydrogen bonds : angle 6.41624 ( 2439) metal coordination : bond 0.00893 ( 7) metal coordination : angle 12.72792 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 367 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6545 (t70) REVERT: A 199 ILE cc_start: 0.8296 (mt) cc_final: 0.7950 (pt) REVERT: A 222 LEU cc_start: 0.8355 (mt) cc_final: 0.8114 (mt) REVERT: A 224 ILE cc_start: 0.7323 (mp) cc_final: 0.7109 (mp) REVERT: A 315 GLU cc_start: 0.7929 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 522 ASP cc_start: 0.8425 (m-30) cc_final: 0.8121 (m-30) REVERT: A 568 LYS cc_start: 0.8390 (mttm) cc_final: 0.7674 (tttp) REVERT: A 611 ASN cc_start: 0.8013 (t0) cc_final: 0.7744 (t0) REVERT: A 640 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6984 (mt-10) REVERT: A 877 MET cc_start: 0.8547 (tpp) cc_final: 0.8332 (tpp) REVERT: A 890 MET cc_start: 0.6759 (mmt) cc_final: 0.6501 (mmt) REVERT: A 925 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6097 (mt-10) REVERT: A 968 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 992 LEU cc_start: 0.8781 (tp) cc_final: 0.8572 (tp) REVERT: A 996 GLU cc_start: 0.7766 (pt0) cc_final: 0.7542 (pt0) REVERT: A 1241 SER cc_start: 0.9063 (t) cc_final: 0.8742 (p) REVERT: A 1251 MET cc_start: 0.7759 (ttp) cc_final: 0.7330 (ttp) REVERT: A 1257 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7859 (mtm) REVERT: A 1408 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7360 (tt) REVERT: A 1507 LEU cc_start: 0.7983 (mt) cc_final: 0.6894 (pt) REVERT: A 1609 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 1661 ILE cc_start: 0.8896 (mp) cc_final: 0.8446 (mt) REVERT: A 1668 SER cc_start: 0.8765 (t) cc_final: 0.8462 (t) REVERT: A 1702 MET cc_start: 0.8094 (mmm) cc_final: 0.7859 (mmm) REVERT: A 1762 ASP cc_start: 0.6551 (m-30) cc_final: 0.5547 (m-30) REVERT: A 1763 MET cc_start: 0.7153 (mmm) cc_final: 0.6652 (tpt) REVERT: A 1789 GLN cc_start: 0.6887 (pm20) cc_final: 0.6406 (tm-30) REVERT: A 1884 LEU cc_start: 0.8246 (tp) cc_final: 0.8023 (tp) REVERT: A 1902 MET cc_start: 0.7970 (mtp) cc_final: 0.7551 (mmm) REVERT: A 1980 LYS cc_start: 0.7131 (mmmt) cc_final: 0.6864 (tptm) REVERT: A 2036 TRP cc_start: 0.9003 (OUTLIER) cc_final: 0.8565 (m100) REVERT: A 2081 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7572 (mp0) outliers start: 70 outliers final: 42 residues processed: 413 average time/residue: 0.2507 time to fit residues: 154.2272 Evaluate side-chains 349 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1609 ILE Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1946 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2036 TRP Chi-restraints excluded: chain A residue 2073 LEU Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 71 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS A 613 GLN A 618 ASN A1227 HIS A2011 GLN ** A2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.154820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134441 restraints weight = 82008.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140148 restraints weight = 35102.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143637 restraints weight = 19535.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.145809 restraints weight = 12802.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.147235 restraints weight = 9413.002| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16463 Z= 0.223 Angle : 0.759 16.545 22272 Z= 0.406 Chirality : 0.043 0.179 2460 Planarity : 0.006 0.107 2828 Dihedral : 8.445 58.489 2234 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.64 % Favored : 85.21 % Rotamer: Outliers : 4.40 % Allowed : 19.79 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.26 % 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 aren not related in a simple way. whole: -2.73 (0.17), residues: 1994 helix: -0.55 (0.15), residues: 1001 sheet: -1.92 (0.42), residues: 114 loop : -3.39 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.022 0.002 TYR A1375 PHE 0.023 0.002 PHE A1518 TRP 0.022 0.002 TRP A 609 HIS 0.008 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00487 (16456) covalent geometry : angle 0.74728 (22270) hydrogen bonds : bond 0.06097 ( 848) hydrogen bonds : angle 6.14978 ( 2439) metal coordination : bond 0.00576 ( 7) metal coordination : angle 14.30466 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 325 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ILE cc_start: 0.7506 (mp) cc_final: 0.7263 (mp) REVERT: A 460 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.6881 (p0) REVERT: A 539 ARG cc_start: 0.8895 (ptm160) cc_final: 0.8574 (ttp80) REVERT: A 543 LEU cc_start: 0.9180 (pp) cc_final: 0.8905 (pp) REVERT: A 547 LYS cc_start: 0.8578 (mttm) cc_final: 0.8305 (mttp) REVERT: A 568 LYS cc_start: 0.8418 (mttm) cc_final: 0.7772 (tttp) REVERT: A 583 MET cc_start: 0.8615 (tpp) cc_final: 0.8305 (mpp) REVERT: A 595 TYR cc_start: 0.8374 (m-80) cc_final: 0.7796 (m-80) REVERT: A 640 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 656 MET cc_start: 0.7590 (mtm) cc_final: 0.6978 (mtm) REVERT: A 790 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6777 (mt-10) REVERT: A 949 ASP cc_start: 0.8231 (m-30) cc_final: 0.7875 (t0) REVERT: A 968 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 992 LEU cc_start: 0.8648 (tp) cc_final: 0.8437 (tp) REVERT: A 996 GLU cc_start: 0.7730 (pt0) cc_final: 0.7508 (pt0) REVERT: A 1031 SER cc_start: 0.9021 (t) cc_final: 0.8814 (p) REVERT: A 1141 ASP cc_start: 0.8041 (t0) cc_final: 0.7773 (t70) REVERT: A 1507 LEU cc_start: 0.8088 (mt) cc_final: 0.6995 (pt) REVERT: A 1626 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7053 (mp0) REVERT: A 1661 ILE cc_start: 0.8972 (mp) cc_final: 0.8574 (mt) REVERT: A 1668 SER cc_start: 0.8753 (t) cc_final: 0.8331 (t) REVERT: A 1676 MET cc_start: 0.7342 (mtp) cc_final: 0.6470 (mtp) REVERT: A 1702 MET cc_start: 0.8265 (mmm) cc_final: 0.8020 (mmm) REVERT: A 1762 ASP cc_start: 0.6733 (m-30) cc_final: 0.5748 (m-30) REVERT: A 1763 MET cc_start: 0.7243 (mmm) cc_final: 0.6791 (tpt) REVERT: A 1789 GLN cc_start: 0.6965 (pm20) cc_final: 0.6445 (tm-30) REVERT: A 1794 TYR cc_start: 0.7341 (t80) cc_final: 0.6780 (t80) REVERT: A 1800 TYR cc_start: 0.5938 (t80) cc_final: 0.5559 (t80) REVERT: A 2036 TRP cc_start: 0.8901 (OUTLIER) cc_final: 0.8662 (m100) outliers start: 79 outliers final: 55 residues processed: 388 average time/residue: 0.2531 time to fit residues: 145.5295 Evaluate side-chains 336 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1105 HIS Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1476 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2036 TRP Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 23 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 192 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 721 GLN A 954 ASN ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.158642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135684 restraints weight = 83678.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141786 restraints weight = 36297.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145570 restraints weight = 20493.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147951 restraints weight = 13589.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.149554 restraints weight = 10049.268| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 16463 Z= 0.268 Angle : 0.774 15.460 22272 Z= 0.415 Chirality : 0.044 0.175 2460 Planarity : 0.006 0.113 2828 Dihedral : 8.041 56.827 2224 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 1.20 % Allowed : 14.39 % Favored : 84.40 % Rotamer: Outliers : 4.79 % Allowed : 20.62 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.26 % 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 aren not related in a simple way. whole: -2.59 (0.18), residues: 1994 helix: -0.38 (0.16), residues: 1008 sheet: -1.73 (0.41), residues: 131 loop : -3.47 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 670 TYR 0.022 0.002 TYR A 879 PHE 0.029 0.002 PHE A 453 TRP 0.020 0.002 TRP A 609 HIS 0.008 0.002 HIS A1296 Details of bonding type rmsd covalent geometry : bond 0.00590 (16456) covalent geometry : angle 0.76128 (22270) hydrogen bonds : bond 0.06279 ( 848) hydrogen bonds : angle 6.09135 ( 2439) metal coordination : bond 0.01855 ( 7) metal coordination : angle 14.62624 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 297 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7623 (mt-10) cc_final: 0.6972 (tm-30) REVERT: A 460 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7047 (p0) REVERT: A 539 ARG cc_start: 0.8894 (ptm160) cc_final: 0.8569 (ttp80) REVERT: A 543 LEU cc_start: 0.9162 (pp) cc_final: 0.8847 (pp) REVERT: A 547 LYS cc_start: 0.8541 (mttm) cc_final: 0.8216 (mttt) REVERT: A 568 LYS cc_start: 0.8391 (mttm) cc_final: 0.7750 (tttt) REVERT: A 595 TYR cc_start: 0.8428 (m-80) cc_final: 0.7657 (m-80) REVERT: A 640 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6781 (mt-10) REVERT: A 656 MET cc_start: 0.7689 (mtm) cc_final: 0.7168 (mtm) REVERT: A 715 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7822 (p0) REVERT: A 768 MET cc_start: 0.7847 (ptp) cc_final: 0.7593 (ptp) REVERT: A 803 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: A 865 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6870 (pt) REVERT: A 902 ASP cc_start: 0.7508 (m-30) cc_final: 0.7258 (m-30) REVERT: A 926 MET cc_start: 0.7817 (mmm) cc_final: 0.6721 (mmm) REVERT: A 949 ASP cc_start: 0.8149 (m-30) cc_final: 0.7697 (t0) REVERT: A 1000 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7136 (tpp80) REVERT: A 1031 SER cc_start: 0.9084 (t) cc_final: 0.8800 (p) REVERT: A 1141 ASP cc_start: 0.7990 (t0) cc_final: 0.7722 (t70) REVERT: A 1215 ARG cc_start: 0.6952 (mtt180) cc_final: 0.6562 (mtm-85) REVERT: A 1241 SER cc_start: 0.8842 (t) cc_final: 0.8290 (p) REVERT: A 1507 LEU cc_start: 0.8113 (mt) cc_final: 0.6992 (pp) REVERT: A 1532 LEU cc_start: 0.8891 (mt) cc_final: 0.8687 (mt) REVERT: A 1546 ARG cc_start: 0.6795 (ttm-80) cc_final: 0.6441 (tpp80) REVERT: A 1626 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7044 (mp0) REVERT: A 1668 SER cc_start: 0.8755 (t) cc_final: 0.8368 (t) REVERT: A 1676 MET cc_start: 0.7376 (mtp) cc_final: 0.6653 (mtp) REVERT: A 1762 ASP cc_start: 0.6632 (m-30) cc_final: 0.5733 (m-30) REVERT: A 1800 TYR cc_start: 0.6588 (t80) cc_final: 0.6026 (t80) REVERT: A 2045 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7908 (t0) outliers start: 86 outliers final: 64 residues processed: 363 average time/residue: 0.2707 time to fit residues: 147.1613 Evaluate side-chains 343 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 715 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 801 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1476 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1973 PHE Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2045 ASN Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN A1048 HIS A1070 HIS ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.162458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139613 restraints weight = 83214.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145841 restraints weight = 35622.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.149679 restraints weight = 19911.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.152129 restraints weight = 13111.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153657 restraints weight = 9620.641| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16463 Z= 0.167 Angle : 0.689 11.198 22272 Z= 0.368 Chirality : 0.041 0.169 2460 Planarity : 0.006 0.113 2828 Dihedral : 7.512 56.495 2219 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.34 % Favored : 85.56 % Rotamer: Outliers : 4.18 % Allowed : 21.40 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.17 (0.18), residues: 1994 helix: 0.00 (0.16), residues: 1010 sheet: -1.73 (0.41), residues: 140 loop : -3.31 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2044 TYR 0.016 0.002 TYR A 551 PHE 0.033 0.002 PHE A 900 TRP 0.019 0.001 TRP A 609 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00361 (16456) covalent geometry : angle 0.68225 (22270) hydrogen bonds : bond 0.05603 ( 848) hydrogen bonds : angle 5.66865 ( 2439) metal coordination : bond 0.00316 ( 7) metal coordination : angle 10.42566 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TRP cc_start: 0.8055 (m-10) cc_final: 0.7528 (m-90) REVERT: A 324 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6854 (tm-30) REVERT: A 460 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.6975 (p0) REVERT: A 539 ARG cc_start: 0.8858 (ptm160) cc_final: 0.8575 (ttp80) REVERT: A 543 LEU cc_start: 0.9108 (pp) cc_final: 0.8762 (pp) REVERT: A 547 LYS cc_start: 0.8524 (mttm) cc_final: 0.8197 (mttt) REVERT: A 568 LYS cc_start: 0.8285 (mttm) cc_final: 0.7718 (tttt) REVERT: A 595 TYR cc_start: 0.8345 (m-80) cc_final: 0.7548 (m-80) REVERT: A 640 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6806 (mt-10) REVERT: A 656 MET cc_start: 0.7636 (mtm) cc_final: 0.7282 (mtm) REVERT: A 715 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7862 (p0) REVERT: A 748 MET cc_start: 0.8432 (tpp) cc_final: 0.8039 (tpp) REVERT: A 768 MET cc_start: 0.7745 (ptp) cc_final: 0.7526 (ptp) REVERT: A 803 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: A 865 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6774 (pt) REVERT: A 949 ASP cc_start: 0.8074 (m-30) cc_final: 0.7545 (t0) REVERT: A 1000 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7128 (tpp80) REVERT: A 1031 SER cc_start: 0.9064 (t) cc_final: 0.8790 (p) REVERT: A 1215 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6702 (mtm-85) REVERT: A 1312 ASP cc_start: 0.6751 (t0) cc_final: 0.6493 (t0) REVERT: A 1507 LEU cc_start: 0.8108 (mt) cc_final: 0.7066 (pt) REVERT: A 1626 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7008 (mp0) REVERT: A 1702 MET cc_start: 0.8323 (mmm) cc_final: 0.8100 (mmm) REVERT: A 1762 ASP cc_start: 0.6721 (m-30) cc_final: 0.5662 (m-30) REVERT: A 1789 GLN cc_start: 0.6746 (tm-30) cc_final: 0.6393 (tm-30) REVERT: A 1800 TYR cc_start: 0.6415 (t80) cc_final: 0.5913 (t80) outliers start: 75 outliers final: 60 residues processed: 351 average time/residue: 0.2599 time to fit residues: 137.3791 Evaluate side-chains 339 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 715 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1280 THR Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138322 restraints weight = 83433.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144404 restraints weight = 35976.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148124 restraints weight = 20280.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.150597 restraints weight = 13500.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152184 restraints weight = 9898.581| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16463 Z= 0.199 Angle : 0.703 11.952 22272 Z= 0.375 Chirality : 0.042 0.150 2460 Planarity : 0.006 0.114 2828 Dihedral : 7.376 56.647 2218 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.69 % Favored : 85.21 % Rotamer: Outliers : 4.63 % Allowed : 20.74 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.06 (0.18), residues: 1994 helix: 0.12 (0.16), residues: 1012 sheet: -1.68 (0.41), residues: 140 loop : -3.30 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 614 TYR 0.016 0.002 TYR A1130 PHE 0.024 0.002 PHE A1518 TRP 0.017 0.001 TRP A 609 HIS 0.011 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00437 (16456) covalent geometry : angle 0.69443 (22270) hydrogen bonds : bond 0.05629 ( 848) hydrogen bonds : angle 5.65734 ( 2439) metal coordination : bond 0.00908 ( 7) metal coordination : angle 11.38387 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 287 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7564 (tpp) cc_final: 0.6930 (ttm) REVERT: A 315 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: A 324 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6882 (tm-30) REVERT: A 460 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.6916 (p0) REVERT: A 539 ARG cc_start: 0.8868 (ptm160) cc_final: 0.8556 (ttp80) REVERT: A 547 LYS cc_start: 0.8599 (mttm) cc_final: 0.8284 (mttt) REVERT: A 568 LYS cc_start: 0.8292 (mttm) cc_final: 0.7767 (tttt) REVERT: A 592 LEU cc_start: 0.2865 (OUTLIER) cc_final: 0.2474 (mt) REVERT: A 595 TYR cc_start: 0.8353 (m-80) cc_final: 0.7530 (m-80) REVERT: A 640 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 656 MET cc_start: 0.7613 (mtm) cc_final: 0.7218 (mtm) REVERT: A 768 MET cc_start: 0.7928 (ptp) cc_final: 0.7619 (ptp) REVERT: A 803 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: A 865 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6799 (pt) REVERT: A 949 ASP cc_start: 0.7999 (m-30) cc_final: 0.7548 (t0) REVERT: A 1031 SER cc_start: 0.9083 (t) cc_final: 0.8819 (p) REVERT: A 1215 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6574 (mtm-85) REVERT: A 1480 MET cc_start: 0.8246 (tpt) cc_final: 0.8022 (tpt) REVERT: A 1507 LEU cc_start: 0.8129 (mt) cc_final: 0.7117 (pt) REVERT: A 1626 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7144 (mp0) REVERT: A 1762 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.5509 (m-30) REVERT: A 1800 TYR cc_start: 0.6691 (t80) cc_final: 0.6251 (t80) REVERT: A 2035 ASN cc_start: 0.8099 (t0) cc_final: 0.7838 (t0) outliers start: 83 outliers final: 65 residues processed: 344 average time/residue: 0.2734 time to fit residues: 141.5794 Evaluate side-chains 341 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1762 ASP Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 1977 LEU Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.160614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138027 restraints weight = 84191.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.144077 restraints weight = 36232.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147859 restraints weight = 20421.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150264 restraints weight = 13473.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151841 restraints weight = 9886.065| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16463 Z= 0.200 Angle : 0.701 15.171 22272 Z= 0.372 Chirality : 0.042 0.148 2460 Planarity : 0.006 0.114 2828 Dihedral : 7.268 56.878 2216 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.54 % Favored : 85.31 % Rotamer: Outliers : 5.02 % Allowed : 20.90 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.98 (0.18), residues: 1994 helix: 0.24 (0.16), residues: 1011 sheet: -1.65 (0.42), residues: 140 loop : -3.32 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 783 TYR 0.019 0.002 TYR A 879 PHE 0.024 0.002 PHE A1518 TRP 0.017 0.001 TRP A 609 HIS 0.009 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00440 (16456) covalent geometry : angle 0.68639 (22270) hydrogen bonds : bond 0.05572 ( 848) hydrogen bonds : angle 5.60064 ( 2439) metal coordination : bond 0.00517 ( 7) metal coordination : angle 15.04512 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7460 (tpp) cc_final: 0.6856 (ttm) REVERT: A 324 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6882 (tm-30) REVERT: A 460 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6822 (p0) REVERT: A 539 ARG cc_start: 0.8857 (ptm160) cc_final: 0.8552 (ttp80) REVERT: A 547 LYS cc_start: 0.8624 (mttm) cc_final: 0.8285 (mttt) REVERT: A 568 LYS cc_start: 0.8311 (mttm) cc_final: 0.7845 (tttt) REVERT: A 592 LEU cc_start: 0.2865 (OUTLIER) cc_final: 0.2495 (mt) REVERT: A 595 TYR cc_start: 0.8336 (m-80) cc_final: 0.7503 (m-80) REVERT: A 640 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6839 (mt-10) REVERT: A 656 MET cc_start: 0.7612 (mtm) cc_final: 0.7224 (mtm) REVERT: A 768 MET cc_start: 0.7982 (ptp) cc_final: 0.7658 (ptp) REVERT: A 865 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6771 (pt) REVERT: A 912 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7731 (tpt170) REVERT: A 944 ASP cc_start: 0.7430 (t0) cc_final: 0.7221 (t0) REVERT: A 949 ASP cc_start: 0.7977 (m-30) cc_final: 0.7522 (t0) REVERT: A 1031 SER cc_start: 0.9060 (t) cc_final: 0.8841 (p) REVERT: A 1507 LEU cc_start: 0.8116 (mt) cc_final: 0.7179 (pt) REVERT: A 1546 ARG cc_start: 0.6837 (ttm-80) cc_final: 0.6371 (tpp80) REVERT: A 1626 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7109 (mp0) REVERT: A 1627 MET cc_start: 0.8739 (mmm) cc_final: 0.8426 (tpt) REVERT: A 1762 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.5523 (m-30) REVERT: A 1800 TYR cc_start: 0.6731 (t80) cc_final: 0.6434 (t80) REVERT: A 2030 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6307 (mp) REVERT: A 2035 ASN cc_start: 0.8068 (t0) cc_final: 0.7822 (t0) outliers start: 90 outliers final: 70 residues processed: 347 average time/residue: 0.2655 time to fit residues: 138.0800 Evaluate side-chains 349 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 273 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1762 ASP Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1887 ILE Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN A1633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.164722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142370 restraints weight = 82834.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.148551 restraints weight = 35264.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152373 restraints weight = 19640.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154775 restraints weight = 12855.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.156376 restraints weight = 9407.405| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16463 Z= 0.142 Angle : 0.658 13.320 22272 Z= 0.348 Chirality : 0.041 0.149 2460 Planarity : 0.005 0.114 2828 Dihedral : 6.834 45.854 2208 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 1.15 % Allowed : 12.64 % Favored : 86.21 % Rotamer: Outliers : 3.90 % Allowed : 22.30 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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 aren not related in a simple way. whole: -1.67 (0.19), residues: 1994 helix: 0.52 (0.16), residues: 1005 sheet: -1.39 (0.43), residues: 139 loop : -3.21 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 482 TYR 0.015 0.001 TYR A1940 PHE 0.024 0.001 PHE A1518 TRP 0.016 0.001 TRP A 609 HIS 0.008 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00311 (16456) covalent geometry : angle 0.64820 (22270) hydrogen bonds : bond 0.05096 ( 848) hydrogen bonds : angle 5.31931 ( 2439) metal coordination : bond 0.00920 ( 7) metal coordination : angle 12.01236 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 299 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.7260 (tpp) cc_final: 0.6684 (ttm) REVERT: A 324 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6861 (tm-30) REVERT: A 333 ARG cc_start: 0.8706 (tpt90) cc_final: 0.8447 (tpt170) REVERT: A 460 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6704 (p0) REVERT: A 539 ARG cc_start: 0.8845 (ptm160) cc_final: 0.8538 (ttp80) REVERT: A 547 LYS cc_start: 0.8608 (mttm) cc_final: 0.8191 (mtmt) REVERT: A 568 LYS cc_start: 0.8244 (mttm) cc_final: 0.7785 (tttt) REVERT: A 640 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6833 (mt-10) REVERT: A 656 MET cc_start: 0.7559 (mtm) cc_final: 0.7134 (mtm) REVERT: A 748 MET cc_start: 0.8389 (tpp) cc_final: 0.8033 (tpp) REVERT: A 766 GLU cc_start: 0.5584 (OUTLIER) cc_final: 0.4853 (mm-30) REVERT: A 768 MET cc_start: 0.7785 (ptp) cc_final: 0.7449 (ptp) REVERT: A 865 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6672 (pt) REVERT: A 912 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7540 (tpt-90) REVERT: A 949 ASP cc_start: 0.7904 (m-30) cc_final: 0.7509 (t0) REVERT: A 1016 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8224 (tp30) REVERT: A 1031 SER cc_start: 0.9038 (t) cc_final: 0.8768 (p) REVERT: A 1113 GLN cc_start: 0.8348 (pm20) cc_final: 0.8120 (pp30) REVERT: A 1507 LEU cc_start: 0.8056 (mt) cc_final: 0.7115 (pt) REVERT: A 1626 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7164 (mp0) REVERT: A 1627 MET cc_start: 0.8743 (mmm) cc_final: 0.8414 (tpt) REVERT: A 1762 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.5790 (m-30) REVERT: A 1800 TYR cc_start: 0.6601 (t80) cc_final: 0.6395 (t80) REVERT: A 2030 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6134 (mp) REVERT: A 2035 ASN cc_start: 0.7999 (t0) cc_final: 0.7774 (t0) outliers start: 70 outliers final: 57 residues processed: 348 average time/residue: 0.2737 time to fit residues: 144.5133 Evaluate side-chains 332 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 269 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1762 ASP Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1887 ILE Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 9 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.138311 restraints weight = 83559.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144345 restraints weight = 36099.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148077 restraints weight = 20345.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150446 restraints weight = 13481.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.152014 restraints weight = 9959.779| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16463 Z= 0.215 Angle : 0.711 15.021 22272 Z= 0.377 Chirality : 0.042 0.147 2460 Planarity : 0.006 0.113 2828 Dihedral : 6.887 47.968 2207 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 1.20 % Allowed : 13.84 % Favored : 84.95 % Rotamer: Outliers : 4.52 % Allowed : 22.35 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % 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 aren not related in a simple way. whole: -1.81 (0.18), residues: 1994 helix: 0.37 (0.16), residues: 1013 sheet: -1.44 (0.42), residues: 141 loop : -3.25 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 652 TYR 0.018 0.002 TYR A2009 PHE 0.026 0.002 PHE A1691 TRP 0.017 0.002 TRP A 609 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00476 (16456) covalent geometry : angle 0.69696 (22270) hydrogen bonds : bond 0.05475 ( 848) hydrogen bonds : angle 5.50245 ( 2439) metal coordination : bond 0.00564 ( 7) metal coordination : angle 15.01856 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 269 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ILE cc_start: 0.7381 (mm) cc_final: 0.7157 (mm) REVERT: A 288 MET cc_start: 0.7390 (tpp) cc_final: 0.6815 (ttm) REVERT: A 324 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6915 (tm-30) REVERT: A 460 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6774 (p0) REVERT: A 539 ARG cc_start: 0.8842 (ptm160) cc_final: 0.8539 (ttp80) REVERT: A 547 LYS cc_start: 0.8623 (mttm) cc_final: 0.8279 (mttt) REVERT: A 568 LYS cc_start: 0.8321 (mttm) cc_final: 0.7843 (tttt) REVERT: A 640 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 656 MET cc_start: 0.7630 (mtm) cc_final: 0.7203 (mtm) REVERT: A 768 MET cc_start: 0.8003 (ptp) cc_final: 0.7720 (ptp) REVERT: A 865 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6742 (pt) REVERT: A 912 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7768 (tpt170) REVERT: A 949 ASP cc_start: 0.7923 (m-30) cc_final: 0.7487 (t0) REVERT: A 1031 SER cc_start: 0.9065 (t) cc_final: 0.8802 (p) REVERT: A 1113 GLN cc_start: 0.8308 (pm20) cc_final: 0.8016 (pp30) REVERT: A 1507 LEU cc_start: 0.8087 (mt) cc_final: 0.7163 (pt) REVERT: A 1546 ARG cc_start: 0.7056 (ttm-80) cc_final: 0.6570 (tpp80) REVERT: A 1626 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7203 (mp0) REVERT: A 1627 MET cc_start: 0.8795 (mmm) cc_final: 0.8463 (tpt) REVERT: A 1762 ASP cc_start: 0.6579 (OUTLIER) cc_final: 0.5619 (m-30) REVERT: A 1800 TYR cc_start: 0.6864 (t80) cc_final: 0.6631 (t80) REVERT: A 2024 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8338 (p) REVERT: A 2030 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6475 (mp) REVERT: A 2035 ASN cc_start: 0.8127 (t0) cc_final: 0.7871 (t0) outliers start: 81 outliers final: 67 residues processed: 328 average time/residue: 0.2963 time to fit residues: 146.1071 Evaluate side-chains 333 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 CYS Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 831 ASN Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1762 ASP Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1887 ILE Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2024 THR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 149 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.165752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143507 restraints weight = 82540.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149683 restraints weight = 34900.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153514 restraints weight = 19394.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155944 restraints weight = 12654.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157350 restraints weight = 9207.044| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16463 Z= 0.138 Angle : 0.661 11.825 22272 Z= 0.348 Chirality : 0.040 0.150 2460 Planarity : 0.005 0.113 2828 Dihedral : 6.637 47.584 2205 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 1.15 % Allowed : 11.94 % Favored : 86.91 % Rotamer: Outliers : 3.34 % Allowed : 23.41 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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 aren not related in a simple way. whole: -1.53 (0.19), residues: 1994 helix: 0.66 (0.16), residues: 1010 sheet: -1.39 (0.43), residues: 137 loop : -3.18 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1454 TYR 0.014 0.001 TYR A 283 PHE 0.024 0.001 PHE A1518 TRP 0.015 0.001 TRP A 609 HIS 0.009 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00300 (16456) covalent geometry : angle 0.65278 (22270) hydrogen bonds : bond 0.04906 ( 848) hydrogen bonds : angle 5.16323 ( 2439) metal coordination : bond 0.00802 ( 7) metal coordination : angle 10.73997 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3988 Ramachandran restraints generated. 1994 Oldfield, 0 Emsley, 1994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.6948 (tpp) cc_final: 0.6643 (ttm) REVERT: A 324 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6846 (tm-30) REVERT: A 333 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8430 (tpt170) REVERT: A 423 LYS cc_start: 0.8372 (ptpt) cc_final: 0.7996 (pttp) REVERT: A 460 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6580 (p0) REVERT: A 539 ARG cc_start: 0.8816 (ptm160) cc_final: 0.8521 (ttp80) REVERT: A 568 LYS cc_start: 0.8228 (mttm) cc_final: 0.7773 (tttt) REVERT: A 640 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 656 MET cc_start: 0.7623 (mtm) cc_final: 0.7244 (mtm) REVERT: A 748 MET cc_start: 0.8370 (tpp) cc_final: 0.8000 (tpp) REVERT: A 766 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.4827 (mm-30) REVERT: A 768 MET cc_start: 0.7728 (ptp) cc_final: 0.7319 (ptp) REVERT: A 865 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6598 (pt) REVERT: A 912 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7568 (tpt-90) REVERT: A 949 ASP cc_start: 0.7689 (m-30) cc_final: 0.7322 (t0) REVERT: A 1016 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8314 (tp30) REVERT: A 1031 SER cc_start: 0.9025 (t) cc_final: 0.8765 (p) REVERT: A 1109 MET cc_start: 0.8641 (ttp) cc_final: 0.8300 (ttm) REVERT: A 1113 GLN cc_start: 0.8219 (pm20) cc_final: 0.8016 (pp30) REVERT: A 1507 LEU cc_start: 0.8120 (mt) cc_final: 0.7352 (pt) REVERT: A 1546 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6449 (tpp80) REVERT: A 1626 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7184 (mp0) REVERT: A 1627 MET cc_start: 0.8753 (mmm) cc_final: 0.8433 (tpt) REVERT: A 1762 ASP cc_start: 0.6729 (m-30) cc_final: 0.6064 (m-30) REVERT: A 1800 TYR cc_start: 0.6675 (t80) cc_final: 0.6472 (t80) REVERT: A 2024 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8359 (p) REVERT: A 2035 ASN cc_start: 0.7969 (t0) cc_final: 0.7762 (t0) outliers start: 60 outliers final: 53 residues processed: 337 average time/residue: 0.2799 time to fit residues: 143.3951 Evaluate side-chains 337 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1130 TYR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1189 PHE Chi-restraints excluded: chain A residue 1194 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1440 ILE Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 2024 THR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 133 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 181 optimal weight: 30.0000 chunk 81 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 618 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.163233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140868 restraints weight = 83359.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.146979 restraints weight = 35794.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.150731 restraints weight = 19995.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.153152 restraints weight = 13172.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.154709 restraints weight = 9635.939| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16463 Z= 0.178 Angle : 0.685 13.563 22272 Z= 0.360 Chirality : 0.041 0.156 2460 Planarity : 0.006 0.113 2828 Dihedral : 6.625 50.708 2204 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 1.00 % Allowed : 12.79 % Favored : 86.21 % Rotamer: Outliers : 3.79 % Allowed : 23.75 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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 aren not related in a simple way. whole: -1.56 (0.19), residues: 1994 helix: 0.63 (0.16), residues: 1009 sheet: -1.37 (0.43), residues: 137 loop : -3.18 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 652 TYR 0.016 0.002 TYR A 879 PHE 0.025 0.002 PHE A1691 TRP 0.016 0.001 TRP A 609 HIS 0.010 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00398 (16456) covalent geometry : angle 0.67345 (22270) hydrogen bonds : bond 0.05129 ( 848) hydrogen bonds : angle 5.29155 ( 2439) metal coordination : bond 0.00230 ( 7) metal coordination : angle 13.05223 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.85 seconds wall clock time: 78 minutes 59.25 seconds (4739.25 seconds total)