Starting phenix.real_space_refine on Fri Jun 27 12:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a22_6337/06_2025/5a22_6337_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a22_6337/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5a22_6337/06_2025/5a22_6337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a22_6337/06_2025/5a22_6337.map" model { file = "/net/cci-nas-00/data/ceres_data/5a22_6337/06_2025/5a22_6337_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a22_6337/06_2025/5a22_6337_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.42, per 1000 atoms: 0.48 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: 9.96 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 4.32 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: 15.99 Time building geometry restraints manager: 12.01 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: 0.110 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: 0.560 Extract box with map and model: 1.360 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 94.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.510 ------------------------------------------------------------------------------- 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 : 14.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.003 TRP A1079 HIS 0.014 0.002 HIS A2067 PHE 0.029 0.003 PHE A1896 TYR 0.037 0.003 TYR A 879 ARG 0.008 0.001 ARG A1396 Details of bonding type rmsd hydrogen bonds : bond 0.12572 ( 848) hydrogen bonds : angle 9.01081 ( 2439) metal coordination : bond 0.14565 ( 7) metal coordination : angle 41.22304 ( 2) covalent geometry : bond 0.00932 (16456) covalent geometry : angle 1.48976 (22270) *********************** 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 : 2.357 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: 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: 0.8345 (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: 0.8447 (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: 0.8113 (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: 0.9037 (mmtt) REVERT: A 414 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (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: 0.7608 (p0) REVERT: A 507 LYS cc_start: 0.8616 (tttt) cc_final: 0.8330 (tptt) REVERT: A 512 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8304 (pt0) REVERT: A 521 ASP cc_start: 0.8705 (m-30) cc_final: 0.8293 (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: 0.8584 (mtmt) 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: 0.7997 (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: 0.7992 (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: 0.8714 (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: 0.8819 (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: 0.8701 (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: 0.6695 (mmt180) REVERT: A 1241 SER cc_start: 0.9479 (t) cc_final: 0.9104 (p) REVERT: A 1257 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: A 1267 PHE cc_start: 0.8398 (p90) cc_final: 0.8146 (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: 0.8063 (mt-10) REVERT: A 1317 TYR cc_start: 0.7807 (t80) cc_final: 0.6947 (t80) REVERT: A 1384 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7714 (m) REVERT: A 1398 ARG cc_start: 0.8325 (ptt180) cc_final: 0.7888 (mtp180) REVERT: A 1408 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (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: 0.8554 (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: 0.8553 (tptt) REVERT: A 1480 MET cc_start: 0.8841 (mmp) cc_final: 0.8549 (mmm) REVERT: A 1507 LEU cc_start: 0.8961 (mt) cc_final: 0.7582 (pt) REVERT: A 1609 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8308 (mt) REVERT: A 1661 ILE cc_start: 0.9167 (mp) cc_final: 0.8633 (mt) REVERT: A 1663 TYR cc_start: 0.9215 (p90) cc_final: 0.8829 (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: 0.7522 (m-30) REVERT: A 1788 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8956 (mp0) REVERT: A 1789 GLN cc_start: 0.8085 (pm20) cc_final: 0.7162 (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: 0.7429 (m-10) REVERT: A 1902 MET cc_start: 0.8634 (mtp) cc_final: 0.8262 (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: 0.7489 (ptm-80) REVERT: A 2092 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.8103 (ttm-80) REVERT: A 2108 ARG cc_start: 0.8802 (mmt90) cc_final: 0.8517 (mmm-85) outliers start: 100 outliers final: 35 residues processed: 530 average time/residue: 0.7517 time to fit residues: 569.2217 Evaluate side-chains 382 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 335 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 168 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.166639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143169 restraints weight = 81583.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149678 restraints weight = 34564.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153721 restraints weight = 19259.541| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16463 Z= 0.209 Angle : 0.816 16.535 22272 Z= 0.438 Chirality : 0.044 0.208 2460 Planarity : 0.006 0.108 2828 Dihedral : 9.619 71.521 2268 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 1.20 % Allowed : 12.89 % Favored : 85.91 % Rotamer: Outliers : 4.24 % Allowed : 17.84 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.26 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.16), residues: 1994 helix: -1.40 (0.14), residues: 995 sheet: -1.93 (0.41), residues: 114 loop : -3.56 (0.18), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1079 HIS 0.006 0.002 HIS A1105 PHE 0.037 0.002 PHE A 219 TYR 0.020 0.002 TYR A1375 ARG 0.005 0.001 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.06590 ( 848) hydrogen bonds : angle 6.51132 ( 2439) metal coordination : bond 0.00897 ( 7) metal coordination : angle 13.04998 ( 2) covalent geometry : bond 0.00452 (16456) covalent geometry : angle 0.80689 (22270) *********************** 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 436 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 360 time to evaluate : 3.211 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: A 117 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6619 (t70) REVERT: A 199 ILE cc_start: 0.8171 (mt) cc_final: 0.7731 (pt) REVERT: A 315 GLU cc_start: 0.8084 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 547 LYS cc_start: 0.8528 (mttm) cc_final: 0.8210 (mttp) REVERT: A 568 LYS cc_start: 0.8441 (mttm) cc_final: 0.7748 (tttp) REVERT: A 611 ASN cc_start: 0.8090 (t0) cc_final: 0.7874 (m-40) REVERT: A 640 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 851 ASP cc_start: 0.8456 (t0) cc_final: 0.8202 (t70) REVERT: A 890 MET cc_start: 0.6755 (mmt) cc_final: 0.6462 (mmt) REVERT: A 968 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 992 LEU cc_start: 0.8768 (tp) cc_final: 0.8567 (tp) REVERT: A 996 GLU cc_start: 0.7845 (pt0) cc_final: 0.7631 (pt0) REVERT: A 1241 SER cc_start: 0.9086 (t) cc_final: 0.8787 (p) REVERT: A 1251 MET cc_start: 0.7853 (ttp) cc_final: 0.7451 (ttp) REVERT: A 1408 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7402 (tt) REVERT: A 1507 LEU cc_start: 0.8010 (mt) cc_final: 0.6904 (pt) REVERT: A 1609 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8110 (mt) REVERT: A 1631 ILE cc_start: 0.6619 (mt) cc_final: 0.6326 (mm) REVERT: A 1661 ILE cc_start: 0.8942 (mp) cc_final: 0.8578 (mt) REVERT: A 1668 SER cc_start: 0.8729 (t) cc_final: 0.8429 (t) REVERT: A 1702 MET cc_start: 0.8152 (mmm) cc_final: 0.7931 (mmm) REVERT: A 1762 ASP cc_start: 0.6374 (m-30) cc_final: 0.5456 (m-30) REVERT: A 1763 MET cc_start: 0.7223 (mmm) cc_final: 0.6711 (tpt) REVERT: A 1789 GLN cc_start: 0.6957 (pm20) cc_final: 0.6307 (tm-30) REVERT: A 1800 TYR cc_start: 0.5947 (t80) cc_final: 0.5639 (t80) REVERT: A 1902 MET cc_start: 0.8024 (mtp) cc_final: 0.7632 (mmm) REVERT: A 2036 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.8578 (m100) REVERT: A 2081 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7514 (mp0) outliers start: 76 outliers final: 49 residues processed: 412 average time/residue: 0.7287 time to fit residues: 450.1038 Evaluate side-chains 344 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 291 time to evaluate : 5.149 ------------------------------------------------------------------------------- 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 377 THR 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 707 VAL 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 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 865 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 1030 ILE 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 1278 ILE 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 1482 VAL 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 190 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 195 HIS A 613 GLN A 618 ASN A2011 GLN A2045 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135067 restraints weight = 81949.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140796 restraints weight = 35037.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144327 restraints weight = 19459.162| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16463 Z= 0.205 Angle : 0.749 15.827 22272 Z= 0.399 Chirality : 0.043 0.178 2460 Planarity : 0.006 0.107 2828 Dihedral : 8.559 68.864 2239 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.54 % Favored : 85.31 % Rotamer: Outliers : 4.52 % Allowed : 19.62 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.17), residues: 1994 helix: -0.51 (0.15), residues: 1002 sheet: -1.94 (0.43), residues: 114 loop : -3.41 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 609 HIS 0.007 0.001 HIS A1105 PHE 0.023 0.002 PHE A 219 TYR 0.021 0.002 TYR A1375 ARG 0.005 0.000 ARG A 482 Details of bonding type rmsd hydrogen bonds : bond 0.06033 ( 848) hydrogen bonds : angle 6.06871 ( 2439) metal coordination : bond 0.00832 ( 7) metal coordination : angle 13.68489 ( 2) covalent geometry : bond 0.00442 (16456) covalent geometry : angle 0.73764 (22270) *********************** 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 407 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 326 time to evaluate : 3.446 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 222 LEU cc_start: 0.8316 (mt) cc_final: 0.8025 (mt) REVERT: A 224 ILE cc_start: 0.7466 (mp) cc_final: 0.7233 (mp) REVERT: A 261 ILE cc_start: 0.8810 (mm) cc_final: 0.8589 (mm) REVERT: A 342 VAL cc_start: 0.8537 (t) cc_final: 0.8323 (p) REVERT: A 460 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.6749 (p0) REVERT: A 539 ARG cc_start: 0.8884 (ptm160) cc_final: 0.8583 (ttp80) REVERT: A 543 LEU cc_start: 0.9227 (pp) cc_final: 0.8959 (pp) REVERT: A 547 LYS cc_start: 0.8564 (mttm) cc_final: 0.8261 (mttp) REVERT: A 568 LYS cc_start: 0.8423 (mttm) cc_final: 0.7801 (tttp) REVERT: A 595 TYR cc_start: 0.8327 (m-80) cc_final: 0.7735 (m-80) REVERT: A 611 ASN cc_start: 0.8080 (t0) cc_final: 0.7831 (m110) REVERT: A 640 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 656 MET cc_start: 0.7615 (mtm) cc_final: 0.7003 (mtm) REVERT: A 803 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: A 851 ASP cc_start: 0.8509 (t0) cc_final: 0.8232 (t70) REVERT: A 877 MET cc_start: 0.8398 (tpp) cc_final: 0.8192 (tpp) REVERT: A 949 ASP cc_start: 0.8310 (m-30) cc_final: 0.7913 (t0) REVERT: A 968 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 992 LEU cc_start: 0.8655 (tp) cc_final: 0.8450 (tp) REVERT: A 996 GLU cc_start: 0.7686 (pt0) cc_final: 0.7430 (pt0) REVERT: A 1031 SER cc_start: 0.9049 (t) cc_final: 0.8773 (p) REVERT: A 1141 ASP cc_start: 0.7999 (t0) cc_final: 0.7738 (t70) REVERT: A 1175 LEU cc_start: 0.8129 (mm) cc_final: 0.7927 (mm) REVERT: A 1507 LEU cc_start: 0.8092 (mt) cc_final: 0.7011 (pt) REVERT: A 1626 GLU cc_start: 0.7881 (mt-10) cc_final: 0.6947 (mp0) REVERT: A 1631 ILE cc_start: 0.7084 (mt) cc_final: 0.6501 (mm) REVERT: A 1633 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7507 (m110) REVERT: A 1668 SER cc_start: 0.8739 (t) cc_final: 0.8319 (t) REVERT: A 1676 MET cc_start: 0.7271 (mtp) cc_final: 0.6176 (mtp) REVERT: A 1702 MET cc_start: 0.8233 (mmm) cc_final: 0.8021 (mmm) REVERT: A 1762 ASP cc_start: 0.6723 (m-30) cc_final: 0.5615 (m-30) REVERT: A 1763 MET cc_start: 0.7170 (mmm) cc_final: 0.6736 (tpt) REVERT: A 1789 GLN cc_start: 0.6964 (pm20) cc_final: 0.6409 (tm-30) REVERT: A 1794 TYR cc_start: 0.7266 (t80) cc_final: 0.6812 (t80) REVERT: A 1800 TYR cc_start: 0.6186 (t80) cc_final: 0.5825 (t80) REVERT: A 1807 ASN cc_start: 0.7512 (m-40) cc_final: 0.6835 (m110) REVERT: A 1980 LYS cc_start: 0.7342 (mmmt) cc_final: 0.6918 (tptm) REVERT: A 2036 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.8708 (m100) outliers start: 81 outliers final: 50 residues processed: 387 average time/residue: 0.8346 time to fit residues: 500.0326 Evaluate side-chains 336 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 HIS Chi-restraints excluded: chain A residue 339 ILE 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 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 803 ASP 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 1437 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 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 1633 ASN Chi-restraints excluded: chain A residue 1636 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 2009 TYR 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 151 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A 721 GLN A 954 ASN A1048 HIS A1227 HIS ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.159030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135919 restraints weight = 84494.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.142036 restraints weight = 36349.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.145845 restraints weight = 20461.331| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 16463 Z= 0.259 Angle : 0.763 14.476 22272 Z= 0.409 Chirality : 0.043 0.166 2460 Planarity : 0.006 0.113 2828 Dihedral : 8.246 70.531 2229 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 1.25 % Allowed : 14.34 % Favored : 84.40 % Rotamer: Outliers : 4.79 % Allowed : 19.96 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 1994 helix: -0.32 (0.16), residues: 1008 sheet: -1.72 (0.42), residues: 126 loop : -3.43 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 609 HIS 0.007 0.002 HIS A1105 PHE 0.028 0.002 PHE A 453 TYR 0.017 0.002 TYR A1663 ARG 0.005 0.001 ARG A 670 Details of bonding type rmsd hydrogen bonds : bond 0.06212 ( 848) hydrogen bonds : angle 6.04081 ( 2439) metal coordination : bond 0.01648 ( 7) metal coordination : angle 13.78043 ( 2) covalent geometry : bond 0.00571 (16456) covalent geometry : angle 0.75226 (22270) *********************** 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 381 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 295 time to evaluate : 2.686 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 324 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6844 (tm-30) REVERT: A 423 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8466 (ptpt) REVERT: A 460 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.6856 (p0) REVERT: A 539 ARG cc_start: 0.8899 (ptm160) cc_final: 0.8602 (ttp80) REVERT: A 543 LEU cc_start: 0.9195 (pp) cc_final: 0.8922 (pp) REVERT: A 547 LYS cc_start: 0.8572 (mttm) cc_final: 0.8267 (mttt) REVERT: A 568 LYS cc_start: 0.8404 (mttm) cc_final: 0.7798 (tttp) REVERT: A 595 TYR cc_start: 0.8372 (m-80) cc_final: 0.7580 (m-80) REVERT: A 640 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 656 MET cc_start: 0.7679 (mtm) cc_final: 0.7109 (mtm) REVERT: A 715 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7876 (p0) REVERT: A 768 MET cc_start: 0.7655 (ptp) cc_final: 0.7366 (ptp) REVERT: A 802 ASN cc_start: 0.8010 (m-40) cc_final: 0.7770 (m-40) REVERT: A 803 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: A 851 ASP cc_start: 0.8526 (t0) cc_final: 0.8242 (t70) REVERT: A 865 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6838 (pt) REVERT: A 892 LEU cc_start: 0.9312 (mp) cc_final: 0.9082 (mm) REVERT: A 902 ASP cc_start: 0.7466 (m-30) cc_final: 0.7209 (m-30) REVERT: A 968 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 1000 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7131 (tpp80) REVERT: A 1031 SER cc_start: 0.9116 (t) cc_final: 0.8804 (p) REVERT: A 1141 ASP cc_start: 0.8016 (t0) cc_final: 0.7701 (t70) REVERT: A 1215 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6400 (mtm-85) REVERT: A 1241 SER cc_start: 0.8931 (t) cc_final: 0.8476 (p) REVERT: A 1507 LEU cc_start: 0.8100 (mt) cc_final: 0.6985 (pp) REVERT: A 1532 LEU cc_start: 0.8901 (mt) cc_final: 0.8691 (mt) REVERT: A 1626 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7174 (mp0) REVERT: A 1668 SER cc_start: 0.8779 (t) cc_final: 0.8428 (t) REVERT: A 1676 MET cc_start: 0.7321 (mtp) cc_final: 0.6271 (mtp) REVERT: A 1762 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.5566 (m-30) REVERT: A 1789 GLN cc_start: 0.7017 (pm20) cc_final: 0.6679 (tm-30) REVERT: A 1794 TYR cc_start: 0.7294 (t80) cc_final: 0.6886 (t80) REVERT: A 1800 TYR cc_start: 0.6427 (t80) cc_final: 0.6210 (t80) REVERT: A 2000 TRP cc_start: 0.7705 (t-100) cc_final: 0.6673 (t-100) outliers start: 86 outliers final: 64 residues processed: 359 average time/residue: 0.6809 time to fit residues: 365.3530 Evaluate side-chains 348 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 2.702 ------------------------------------------------------------------------------- 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 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 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 662 THR 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 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 953 LEU 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 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 1480 MET 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 1621 TYR Chi-restraints excluded: chain A residue 1633 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1762 ASP 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 1974 TRP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A2045 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.158686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135942 restraints weight = 83890.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141925 restraints weight = 36039.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145675 restraints weight = 20339.504| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16463 Z= 0.240 Angle : 0.737 12.786 22272 Z= 0.395 Chirality : 0.043 0.165 2460 Planarity : 0.006 0.113 2828 Dihedral : 7.933 72.613 2224 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.54 % Favored : 84.30 % Rotamer: Outliers : 4.91 % Allowed : 20.57 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 1994 helix: -0.19 (0.16), residues: 1019 sheet: -1.87 (0.41), residues: 138 loop : -3.39 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 609 HIS 0.008 0.001 HIS A2102 PHE 0.027 0.002 PHE A 900 TYR 0.019 0.002 TYR A 879 ARG 0.004 0.000 ARG A 614 Details of bonding type rmsd hydrogen bonds : bond 0.06073 ( 848) hydrogen bonds : angle 5.89080 ( 2439) metal coordination : bond 0.01308 ( 7) metal coordination : angle 12.71631 ( 2) covalent geometry : bond 0.00523 (16456) covalent geometry : angle 0.72668 (22270) *********************** 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 377 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 289 time to evaluate : 2.831 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: A 286 ILE cc_start: 0.7558 (mm) cc_final: 0.7326 (mm) REVERT: A 324 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6924 (tm-30) REVERT: A 460 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.6974 (p0) REVERT: A 539 ARG cc_start: 0.8872 (ptm160) cc_final: 0.8581 (ttp80) REVERT: A 543 LEU cc_start: 0.9226 (pp) cc_final: 0.8926 (pp) REVERT: A 547 LYS cc_start: 0.8596 (mttm) cc_final: 0.8279 (mttt) REVERT: A 568 LYS cc_start: 0.8427 (mttm) cc_final: 0.7814 (tttp) REVERT: A 595 TYR cc_start: 0.8376 (m-80) cc_final: 0.7505 (m-80) REVERT: A 625 MET cc_start: 0.7747 (tpp) cc_final: 0.7526 (tpp) REVERT: A 640 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 656 MET cc_start: 0.7690 (mtm) cc_final: 0.7299 (mtm) REVERT: A 715 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 768 MET cc_start: 0.7841 (ptp) cc_final: 0.7517 (ptp) REVERT: A 851 ASP cc_start: 0.8505 (t0) cc_final: 0.8219 (t70) REVERT: A 865 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6726 (pt) REVERT: A 892 LEU cc_start: 0.9320 (mp) cc_final: 0.9045 (mm) REVERT: A 968 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7693 (mm-30) REVERT: A 1031 SER cc_start: 0.9120 (t) cc_final: 0.8793 (p) REVERT: A 1062 SER cc_start: 0.7780 (OUTLIER) cc_final: 0.7573 (t) REVERT: A 1215 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6692 (mtm-85) REVERT: A 1507 LEU cc_start: 0.8130 (mt) cc_final: 0.7071 (pp) REVERT: A 1546 ARG cc_start: 0.6853 (ttm-80) cc_final: 0.6441 (tpp80) REVERT: A 1626 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7115 (mp0) REVERT: A 1762 ASP cc_start: 0.6559 (m-30) cc_final: 0.5603 (m-30) REVERT: A 1794 TYR cc_start: 0.7303 (t80) cc_final: 0.6828 (t80) REVERT: A 1807 ASN cc_start: 0.7671 (m-40) cc_final: 0.7054 (m110) REVERT: A 2024 THR cc_start: 0.8795 (m) cc_final: 0.8489 (p) REVERT: A 2045 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7941 (t0) outliers start: 88 outliers final: 72 residues processed: 352 average time/residue: 0.7073 time to fit residues: 373.6148 Evaluate side-chains 347 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 270 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 223 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 262 PHE 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 336 HIS 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 496 GLN 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 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 891 SER 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 1062 SER 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 1480 MET 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 1621 TYR Chi-restraints excluded: chain A residue 1633 ASN Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 ASP 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 1974 TRP Chi-restraints excluded: chain A residue 1998 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2045 ASN Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2077 THR Chi-restraints excluded: chain A residue 2099 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 GLN A1070 HIS A1236 HIS A2045 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.162114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.139221 restraints weight = 83356.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.145338 restraints weight = 35896.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.149157 restraints weight = 20166.902| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16463 Z= 0.167 Angle : 0.691 13.801 22272 Z= 0.366 Chirality : 0.041 0.148 2460 Planarity : 0.006 0.114 2828 Dihedral : 7.640 70.240 2222 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.79 % Favored : 86.11 % Rotamer: Outliers : 4.35 % Allowed : 20.90 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1994 helix: 0.12 (0.16), residues: 1013 sheet: -1.71 (0.41), residues: 139 loop : -3.29 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 609 HIS 0.006 0.001 HIS A 603 PHE 0.023 0.001 PHE A 900 TYR 0.018 0.002 TYR A1800 ARG 0.004 0.000 ARG A2044 Details of bonding type rmsd hydrogen bonds : bond 0.05546 ( 848) hydrogen bonds : angle 5.58393 ( 2439) metal coordination : bond 0.00804 ( 7) metal coordination : angle 13.77286 ( 2) covalent geometry : bond 0.00362 (16456) covalent geometry : angle 0.67817 (22270) *********************** 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 376 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 3.671 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 286 ILE cc_start: 0.7411 (mm) cc_final: 0.7194 (mm) REVERT: A 288 MET cc_start: 0.7458 (tpp) cc_final: 0.6818 (ttm) REVERT: A 324 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6854 (tm-30) REVERT: A 460 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.6902 (p0) REVERT: A 520 ASP cc_start: 0.8364 (p0) cc_final: 0.8152 (p0) REVERT: A 539 ARG cc_start: 0.8833 (ptm160) cc_final: 0.8574 (ttp80) REVERT: A 547 LYS cc_start: 0.8595 (mttm) cc_final: 0.8275 (mttt) REVERT: A 568 LYS cc_start: 0.8295 (mttm) cc_final: 0.7804 (tttt) REVERT: A 592 LEU cc_start: 0.2862 (OUTLIER) cc_final: 0.2500 (mt) REVERT: A 640 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 656 MET cc_start: 0.7603 (mtm) cc_final: 0.7217 (mtm) REVERT: A 715 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 768 MET cc_start: 0.7723 (ptp) cc_final: 0.7400 (ptp) REVERT: A 851 ASP cc_start: 0.8408 (t0) cc_final: 0.8169 (t70) REVERT: A 865 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6763 (pt) REVERT: A 949 ASP cc_start: 0.8207 (m-30) cc_final: 0.7651 (t0) REVERT: A 1031 SER cc_start: 0.9104 (t) cc_final: 0.8787 (p) REVERT: A 1215 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6739 (mtm-85) REVERT: A 1507 LEU cc_start: 0.8068 (mt) cc_final: 0.7121 (pt) REVERT: A 1626 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7097 (mp0) REVERT: A 1627 MET cc_start: 0.8373 (tpt) cc_final: 0.8150 (tpt) REVERT: A 1762 ASP cc_start: 0.6686 (m-30) cc_final: 0.5588 (m-30) REVERT: A 1763 MET cc_start: 0.7270 (tpt) cc_final: 0.7062 (tpt) REVERT: A 1800 TYR cc_start: 0.5967 (t80) cc_final: 0.5417 (t80) REVERT: A 1807 ASN cc_start: 0.7665 (m-40) cc_final: 0.7330 (m110) outliers start: 78 outliers final: 65 residues processed: 353 average time/residue: 0.6880 time to fit residues: 371.5890 Evaluate side-chains 341 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 272 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 336 HIS 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 466 SER 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 524 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU 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 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 967 THR 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 1426 LYS 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 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 1621 TYR Chi-restraints excluded: chain A residue 1633 ASN 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 1775 GLU 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 2029 SER Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2077 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 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 52 ASN A 618 ASN ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2076 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.158092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135410 restraints weight = 84119.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.141389 restraints weight = 36420.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145125 restraints weight = 20534.954| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 16463 Z= 0.268 Angle : 0.758 17.084 22272 Z= 0.403 Chirality : 0.043 0.148 2460 Planarity : 0.006 0.114 2828 Dihedral : 7.732 68.647 2222 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 1.10 % Allowed : 14.64 % Favored : 84.25 % Rotamer: Outliers : 5.35 % Allowed : 20.62 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 1994 helix: -0.03 (0.16), residues: 1015 sheet: -1.73 (0.42), residues: 139 loop : -3.43 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 609 HIS 0.007 0.002 HIS A 603 PHE 0.021 0.002 PHE A1691 TYR 0.022 0.002 TYR A 879 ARG 0.005 0.001 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.06030 ( 848) hydrogen bonds : angle 5.85299 ( 2439) metal coordination : bond 0.00792 ( 7) metal coordination : angle 16.64026 ( 2) covalent geometry : bond 0.00593 (16456) covalent geometry : angle 0.74100 (22270) *********************** 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 375 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 279 time to evaluate : 2.411 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: A 260 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7425 (t0) REVERT: A 286 ILE cc_start: 0.7556 (mm) cc_final: 0.7325 (mm) REVERT: A 288 MET cc_start: 0.7732 (tpp) cc_final: 0.7077 (ttm) REVERT: A 315 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7882 (tm-30) REVERT: A 324 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6854 (tm-30) REVERT: A 460 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.6931 (p0) REVERT: A 539 ARG cc_start: 0.8875 (ptm160) cc_final: 0.8588 (ttp80) REVERT: A 547 LYS cc_start: 0.8630 (mttm) cc_final: 0.8355 (mttt) REVERT: A 568 LYS cc_start: 0.8440 (mttm) cc_final: 0.7933 (tttt) REVERT: A 592 LEU cc_start: 0.2858 (OUTLIER) cc_final: 0.2467 (mt) REVERT: A 611 ASN cc_start: 0.8476 (t0) cc_final: 0.8276 (t0) REVERT: A 640 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6927 (mt-10) REVERT: A 656 MET cc_start: 0.7724 (mtm) cc_final: 0.7295 (mtm) REVERT: A 768 MET cc_start: 0.8019 (ptp) cc_final: 0.7646 (ptp) REVERT: A 865 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6829 (pt) REVERT: A 912 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7792 (tpt170) REVERT: A 949 ASP cc_start: 0.8205 (m-30) cc_final: 0.7641 (t0) REVERT: A 1031 SER cc_start: 0.9134 (t) cc_final: 0.8793 (p) REVERT: A 1507 LEU cc_start: 0.8117 (mt) cc_final: 0.7197 (pt) REVERT: A 1546 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6479 (tpp80) REVERT: A 1626 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7258 (mp0) REVERT: A 1762 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5441 (m-30) REVERT: A 1794 TYR cc_start: 0.7372 (t80) cc_final: 0.6884 (t80) REVERT: A 1800 TYR cc_start: 0.6375 (t80) cc_final: 0.5858 (t80) REVERT: A 2035 ASN cc_start: 0.8435 (t0) cc_final: 0.8070 (t0) outliers start: 96 outliers final: 80 residues processed: 348 average time/residue: 0.6473 time to fit residues: 341.2635 Evaluate side-chains 352 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 266 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 60 LEU 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 223 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 336 HIS 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 466 SER 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 515 GLU 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 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 766 GLU Chi-restraints excluded: chain A residue 770 SER 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 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 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 1495 ILE Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE 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 1633 ASN Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1762 ASP 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 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 2049 LEU Chi-restraints excluded: chain A residue 2076 ASN 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 0 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 618 ASN A1113 GLN ** A1236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.157425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134805 restraints weight = 84343.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140677 restraints weight = 36406.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144371 restraints weight = 20645.511| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 16463 Z= 0.276 Angle : 0.766 16.541 22272 Z= 0.408 Chirality : 0.043 0.147 2460 Planarity : 0.006 0.115 2828 Dihedral : 7.619 69.347 2218 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 1.10 % Allowed : 14.44 % Favored : 84.45 % Rotamer: Outliers : 5.30 % Allowed : 21.01 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 1994 helix: -0.06 (0.16), residues: 1014 sheet: -1.77 (0.41), residues: 141 loop : -3.49 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 609 HIS 0.008 0.002 HIS A 850 PHE 0.021 0.002 PHE A1691 TYR 0.030 0.002 TYR A 879 ARG 0.005 0.001 ARG A 670 Details of bonding type rmsd hydrogen bonds : bond 0.06069 ( 848) hydrogen bonds : angle 5.91019 ( 2439) metal coordination : bond 0.01073 ( 7) metal coordination : angle 16.49712 ( 2) covalent geometry : bond 0.00608 (16456) covalent geometry : angle 0.74947 (22270) *********************** 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 362 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 267 time to evaluate : 2.694 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 260 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7530 (t0) REVERT: A 288 MET cc_start: 0.7769 (tpp) cc_final: 0.7114 (ttm) REVERT: A 315 GLU cc_start: 0.8451 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 324 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6906 (tm-30) REVERT: A 460 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.6902 (p0) REVERT: A 507 LYS cc_start: 0.8066 (tttt) cc_final: 0.7826 (tppt) REVERT: A 539 ARG cc_start: 0.8865 (ptm160) cc_final: 0.8567 (ttp80) REVERT: A 543 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8924 (pp) REVERT: A 547 LYS cc_start: 0.8647 (mttm) cc_final: 0.8337 (mttt) REVERT: A 592 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2492 (mt) REVERT: A 640 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6943 (mt-10) REVERT: A 656 MET cc_start: 0.7765 (mtm) cc_final: 0.7338 (mtm) REVERT: A 748 MET cc_start: 0.8800 (tpp) cc_final: 0.8581 (tpp) REVERT: A 768 MET cc_start: 0.8067 (ptp) cc_final: 0.7651 (ptp) REVERT: A 865 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6887 (pt) REVERT: A 912 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7795 (tpt170) REVERT: A 926 MET cc_start: 0.7668 (mmm) cc_final: 0.6345 (mmm) REVERT: A 949 ASP cc_start: 0.8190 (m-30) cc_final: 0.7614 (t0) REVERT: A 1031 SER cc_start: 0.9127 (t) cc_final: 0.8778 (p) REVERT: A 1480 MET cc_start: 0.8288 (tpt) cc_final: 0.8064 (tpt) REVERT: A 1507 LEU cc_start: 0.8186 (mt) cc_final: 0.7321 (pt) REVERT: A 1626 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7184 (mp0) REVERT: A 1762 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5462 (m-30) REVERT: A 1794 TYR cc_start: 0.7448 (t80) cc_final: 0.6789 (t80) REVERT: A 1800 TYR cc_start: 0.6696 (t80) cc_final: 0.6182 (t80) REVERT: A 2024 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8480 (p) REVERT: A 2030 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6389 (mp) REVERT: A 2035 ASN cc_start: 0.8377 (t0) cc_final: 0.7962 (t0) outliers start: 95 outliers final: 77 residues processed: 335 average time/residue: 0.6432 time to fit residues: 324.9077 Evaluate side-chains 347 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 261 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 60 LEU 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 223 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 336 HIS 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 466 SER 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 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 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 766 GLU Chi-restraints excluded: chain A residue 767 THR 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 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 972 CYS Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1043 PHE 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 1505 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE 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 1633 ASN Chi-restraints excluded: chain A residue 1714 GLU Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 ASP 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 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 2049 LEU Chi-restraints excluded: chain A residue 2053 ASN 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 188 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN A1236 HIS ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136639 restraints weight = 83827.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142606 restraints weight = 36266.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.146328 restraints weight = 20513.229| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16463 Z= 0.213 Angle : 0.726 14.686 22272 Z= 0.385 Chirality : 0.042 0.163 2460 Planarity : 0.006 0.116 2828 Dihedral : 7.479 68.304 2216 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.19 % Favored : 84.65 % Rotamer: Outliers : 4.79 % Allowed : 21.74 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.18), residues: 1994 helix: 0.10 (0.16), residues: 1011 sheet: -1.71 (0.42), residues: 139 loop : -3.42 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 609 HIS 0.008 0.001 HIS A 850 PHE 0.024 0.002 PHE A1826 TYR 0.018 0.002 TYR A 879 ARG 0.004 0.000 ARG A2075 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 848) hydrogen bonds : angle 5.70340 ( 2439) metal coordination : bond 0.00435 ( 7) metal coordination : angle 14.57641 ( 2) covalent geometry : bond 0.00469 (16456) covalent geometry : angle 0.71317 (22270) *********************** 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 361 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 2.465 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 288 MET cc_start: 0.7702 (tpp) cc_final: 0.7054 (ttm) REVERT: A 324 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6832 (tm-30) REVERT: A 460 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6850 (p0) REVERT: A 539 ARG cc_start: 0.8853 (ptm160) cc_final: 0.8503 (ttp80) REVERT: A 543 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8914 (pp) REVERT: A 592 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2484 (mt) REVERT: A 640 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 656 MET cc_start: 0.7722 (mtm) cc_final: 0.7268 (mtm) REVERT: A 748 MET cc_start: 0.8758 (tpp) cc_final: 0.8527 (tpp) REVERT: A 768 MET cc_start: 0.7945 (ptp) cc_final: 0.7504 (ptp) REVERT: A 865 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6902 (pt) REVERT: A 912 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7766 (tpt170) REVERT: A 949 ASP cc_start: 0.7991 (m-30) cc_final: 0.7579 (t0) REVERT: A 1031 SER cc_start: 0.9135 (t) cc_final: 0.8813 (p) REVERT: A 1480 MET cc_start: 0.8325 (tpt) cc_final: 0.8122 (tpt) REVERT: A 1507 LEU cc_start: 0.8197 (mt) cc_final: 0.7352 (pt) REVERT: A 1626 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7169 (mp0) REVERT: A 1762 ASP cc_start: 0.6199 (m-30) cc_final: 0.5467 (m-30) REVERT: A 1800 TYR cc_start: 0.6674 (t80) cc_final: 0.6212 (t80) REVERT: A 2024 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 2030 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6443 (mp) REVERT: A 2035 ASN cc_start: 0.8433 (t0) cc_final: 0.8051 (t0) outliers start: 86 outliers final: 72 residues processed: 339 average time/residue: 0.6550 time to fit residues: 337.4363 Evaluate side-chains 339 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 4.112 ------------------------------------------------------------------------------- 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 328 ILE Chi-restraints excluded: chain A residue 336 HIS 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 466 SER 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 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU 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 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 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 972 CYS 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 1505 SER Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1516 ILE Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1621 TYR Chi-restraints excluded: chain A residue 1633 ASN Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 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 2024 THR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2049 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 199 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** 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 = 0.4140 r_free = 0.4140 target = 0.164467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.142097 restraints weight = 82048.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148189 restraints weight = 35050.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151939 restraints weight = 19570.151| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16463 Z= 0.146 Angle : 0.684 11.519 22272 Z= 0.360 Chirality : 0.041 0.155 2460 Planarity : 0.006 0.116 2828 Dihedral : 7.204 63.315 2216 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 1.15 % Allowed : 12.19 % Favored : 86.66 % Rotamer: Outliers : 3.85 % Allowed : 22.97 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1994 helix: 0.40 (0.16), residues: 1008 sheet: -1.67 (0.43), residues: 137 loop : -3.26 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2000 HIS 0.007 0.001 HIS A 850 PHE 0.020 0.001 PHE A1691 TYR 0.015 0.002 TYR A 283 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 848) hydrogen bonds : angle 5.34869 ( 2439) metal coordination : bond 0.00681 ( 7) metal coordination : angle 10.85912 ( 2) covalent geometry : bond 0.00321 (16456) covalent geometry : angle 0.67605 (22270) ********************** 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 374 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 4.892 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: A 71 TRP cc_start: 0.8138 (m-10) cc_final: 0.7765 (m-90) REVERT: A 288 MET cc_start: 0.7327 (tpp) cc_final: 0.6719 (ttm) REVERT: A 324 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6829 (tm-30) REVERT: A 460 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.6795 (p0) REVERT: A 539 ARG cc_start: 0.8831 (ptm160) cc_final: 0.8536 (ttp80) REVERT: A 640 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6934 (mt-10) REVERT: A 656 MET cc_start: 0.7653 (mtm) cc_final: 0.7201 (mtm) REVERT: A 766 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5356 (mm-30) REVERT: A 768 MET cc_start: 0.7826 (ptp) cc_final: 0.7303 (ptp) REVERT: A 912 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7571 (tpt170) REVERT: A 949 ASP cc_start: 0.7818 (m-30) cc_final: 0.7463 (t0) REVERT: A 1031 SER cc_start: 0.9128 (t) cc_final: 0.8790 (p) REVERT: A 1034 GLN cc_start: 0.6417 (tt0) cc_final: 0.5936 (tp40) REVERT: A 1241 SER cc_start: 0.8864 (t) cc_final: 0.8575 (m) REVERT: A 1251 MET cc_start: 0.7655 (ttp) cc_final: 0.7438 (ttp) REVERT: A 1507 LEU cc_start: 0.8170 (mt) cc_final: 0.7426 (pt) REVERT: A 1546 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6522 (tpp80) REVERT: A 1626 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 1762 ASP cc_start: 0.6888 (m-30) cc_final: 0.5757 (m-30) REVERT: A 1800 TYR cc_start: 0.6422 (t80) cc_final: 0.5999 (t80) REVERT: A 1836 MET cc_start: 0.7607 (tmm) cc_final: 0.6922 (tmm) REVERT: A 1855 ILE cc_start: 0.7559 (mt) cc_final: 0.7306 (mt) REVERT: A 2030 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6244 (mp) REVERT: A 2035 ASN cc_start: 0.8019 (t0) cc_final: 0.7780 (t0) outliers start: 69 outliers final: 57 residues processed: 355 average time/residue: 0.9508 time to fit residues: 535.1018 Evaluate side-chains 337 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 2.631 ------------------------------------------------------------------------------- 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 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 328 ILE Chi-restraints excluded: chain A residue 336 HIS 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 466 SER Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 515 GLU 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 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 720 THR 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 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 972 CYS 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 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1505 SER Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1633 ASN 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 1998 ILE Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2049 LEU 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 186 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 143 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 4.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138825 restraints weight = 83447.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144886 restraints weight = 35944.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.148641 restraints weight = 20216.383| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16463 Z= 0.191 Angle : 0.707 13.488 22272 Z= 0.372 Chirality : 0.041 0.151 2460 Planarity : 0.006 0.113 2828 Dihedral : 7.127 60.053 2210 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.39 % Favored : 85.51 % Rotamer: Outliers : 3.90 % Allowed : 23.47 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 1994 helix: 0.39 (0.16), residues: 1008 sheet: -1.67 (0.43), residues: 137 loop : -3.31 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 609 HIS 0.007 0.001 HIS A 850 PHE 0.024 0.002 PHE A1691 TYR 0.017 0.002 TYR A2009 ARG 0.003 0.000 ARG A2075 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 848) hydrogen bonds : angle 5.45438 ( 2439) metal coordination : bond 0.00289 ( 7) metal coordination : angle 13.35148 ( 2) covalent geometry : bond 0.00426 (16456) covalent geometry : angle 0.69583 (22270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11177.97 seconds wall clock time: 200 minutes 30.68 seconds (12030.68 seconds total)