Starting phenix.real_space_refine on Fri Mar 22 02:44:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_6337_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_6337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_6337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_6337_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a22_6337/03_2024/5a22_6337_neut.pdb" } 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 Residue "A GLU 115": "OE1" <-> "OE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32187 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 32187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2004, 32187 Unusual residues: {' ZN': 2} Classifications: {'peptide': 2002, 'undetermined': 2} Link IDs: {'PTRANS': 93, 'TRANS': 1908, None: 2} Not linked: pdbres="ASP A2109 " pdbres=" ZN A3000 " Not linked: pdbres=" ZN A3000 " pdbres=" ZN A3001 " Chain breaks: 3 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: 14.43, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 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: 26.33 Conformation dependent library (CDL) restraints added in 3.1 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: 2.64 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: 13.73 Time building geometry restraints manager: 27.45 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: 97.43 - 105.40: 395 105.40 - 113.38: 38379 113.38 - 121.36: 13303 121.36 - 129.34: 6621 129.34 - 137.32: 171 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 1.850 nonbonded pdb=" H SER A 471 " pdb=" O MET A 544 " model vdw 1.491 1.850 nonbonded pdb=" O SER A 354 " pdb=" H ARG A 356 " model vdw 1.539 1.850 nonbonded pdb=" O LEU A 629 " pdb=" H TYR A 631 " model vdw 1.546 1.850 nonbonded pdb=" O THR A1254 " pdb=" H MET A1257 " model vdw 1.557 1.850 ... (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: 0.080 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: 0.520 Extract box with map and model: 2.650 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 111.830 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.020 ------------------------------------------------------------------------------- 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 : 0.009 0.081 16456 Z= 0.606 Angle : 1.490 12.317 22270 Z= 0.976 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 *********************** 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 fitting. rotamer outliers: 100 poor density : 457 time to evaluate : 2.350 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: 0.7477 time to fit residues: 562.7321 Evaluate side-chains 382 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 335 time to evaluate : 2.592 ------------------------------------------------------------------------------- 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: 8.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 425 HIS A 618 ASN A 856 GLN A 954 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16456 Z= 0.305 Angle : 0.799 8.260 22270 Z= 0.432 Chirality : 0.044 0.203 2460 Planarity : 0.006 0.106 2828 Dihedral : 9.598 70.425 2268 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 1.20 % Allowed : 13.04 % Favored : 85.76 % Rotamer: Outliers : 4.29 % Allowed : 18.12 % Favored : 77.59 % 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: -3.59 (0.16), residues: 1994 helix: -1.46 (0.14), residues: 1009 sheet: -1.91 (0.41), residues: 113 loop : -3.63 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1079 HIS 0.007 0.002 HIS A1105 PHE 0.037 0.002 PHE A 219 TYR 0.019 0.002 TYR A1375 ARG 0.004 0.001 ARG A2025 *********************** 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 430 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 353 time to evaluate : 2.539 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: A 76 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8103 (mt-10) REVERT: A 147 TRP cc_start: 0.8671 (m100) cc_final: 0.8341 (m100) REVERT: A 172 ASN cc_start: 0.8324 (t0) cc_final: 0.8040 (t0) REVERT: A 199 ILE cc_start: 0.8673 (mt) cc_final: 0.8250 (pt) REVERT: A 295 LEU cc_start: 0.9085 (tp) cc_final: 0.8864 (tt) REVERT: A 315 GLU cc_start: 0.9336 (tt0) cc_final: 0.8695 (tm-30) REVERT: A 422 PHE cc_start: 0.7267 (t80) cc_final: 0.6915 (t80) REVERT: A 459 LEU cc_start: 0.8500 (mt) cc_final: 0.8152 (mt) REVERT: A 460 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 547 LYS cc_start: 0.9004 (mttm) cc_final: 0.8789 (mttp) REVERT: A 551 TYR cc_start: 0.9336 (t80) cc_final: 0.9089 (t80) REVERT: A 568 LYS cc_start: 0.8792 (mttm) cc_final: 0.8012 (tttp) REVERT: A 574 ASP cc_start: 0.6657 (m-30) cc_final: 0.6400 (m-30) REVERT: A 576 LEU cc_start: 0.9156 (tp) cc_final: 0.8717 (tt) REVERT: A 611 ASN cc_start: 0.9009 (t0) cc_final: 0.8507 (m-40) REVERT: A 640 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8350 (mt-10) REVERT: A 764 ASP cc_start: 0.8642 (m-30) cc_final: 0.8164 (t0) REVERT: A 776 TYR cc_start: 0.8734 (t80) cc_final: 0.8452 (t80) REVERT: A 851 ASP cc_start: 0.8882 (t0) cc_final: 0.8630 (t70) REVERT: A 968 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8728 (mm-30) REVERT: A 1007 ASN cc_start: 0.7974 (p0) cc_final: 0.7613 (m-40) REVERT: A 1077 LYS cc_start: 0.9111 (mttt) cc_final: 0.8739 (mmtp) REVERT: A 1137 ASP cc_start: 0.9003 (t0) cc_final: 0.8628 (t0) REVERT: A 1228 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6543 (tpt170) REVERT: A 1251 MET cc_start: 0.8852 (ttp) cc_final: 0.8479 (ttp) REVERT: A 1308 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 1398 ARG cc_start: 0.8256 (ptt180) cc_final: 0.7858 (mtp180) REVERT: A 1408 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 1507 LEU cc_start: 0.9014 (mt) cc_final: 0.7623 (pt) REVERT: A 1512 ASP cc_start: 0.5125 (m-30) cc_final: 0.4597 (t70) REVERT: A 1609 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 1631 ILE cc_start: 0.6982 (mt) cc_final: 0.6615 (mm) REVERT: A 1661 ILE cc_start: 0.9231 (mp) cc_final: 0.8769 (mt) REVERT: A 1663 TYR cc_start: 0.9117 (p90) cc_final: 0.8814 (p90) REVERT: A 1668 SER cc_start: 0.9362 (t) cc_final: 0.9055 (t) REVERT: A 1676 MET cc_start: 0.8992 (mtp) cc_final: 0.8771 (mtp) REVERT: A 1708 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8764 (mm-30) REVERT: A 1762 ASP cc_start: 0.7679 (m-30) cc_final: 0.6771 (m-30) REVERT: A 1763 MET cc_start: 0.8785 (mmm) cc_final: 0.8298 (tpt) REVERT: A 1765 VAL cc_start: 0.8599 (t) cc_final: 0.8346 (m) REVERT: A 1789 GLN cc_start: 0.8019 (pm20) cc_final: 0.7192 (tm-30) REVERT: A 1800 TYR cc_start: 0.7694 (t80) cc_final: 0.7377 (t80) REVERT: A 1807 ASN cc_start: 0.8808 (m-40) cc_final: 0.8472 (m-40) REVERT: A 1869 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7964 (tp30) REVERT: A 1902 MET cc_start: 0.8620 (mtp) cc_final: 0.8138 (mmm) REVERT: A 1980 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7379 (tptm) REVERT: A 2035 ASN cc_start: 0.8876 (m-40) cc_final: 0.8595 (t0) REVERT: A 2036 TRP cc_start: 0.9432 (OUTLIER) cc_final: 0.9128 (m100) REVERT: A 2046 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8261 (tp-100) REVERT: A 2074 ARG cc_start: 0.7725 (tpt90) cc_final: 0.7363 (ttm-80) REVERT: A 2081 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8114 (mp0) REVERT: A 2086 ARG cc_start: 0.7308 (ptm-80) cc_final: 0.6887 (ptm-80) outliers start: 77 outliers final: 53 residues processed: 410 average time/residue: 0.6460 time to fit residues: 391.0377 Evaluate side-chains 355 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 298 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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 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 321 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 763 ASN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 772 ASP 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 881 ASP 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 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 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 1495 ILE 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 1636 LEU 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 2009 TYR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2036 TRP Chi-restraints excluded: chain A residue 2053 ASN Chi-restraints excluded: chain A residue 2073 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 618 ASN ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16456 Z= 0.366 Angle : 0.776 8.718 22270 Z= 0.420 Chirality : 0.044 0.183 2460 Planarity : 0.006 0.109 2828 Dihedral : 8.680 61.061 2240 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 1.15 % Allowed : 15.10 % Favored : 83.75 % Rotamer: Outliers : 4.85 % Allowed : 19.29 % 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: -2.91 (0.17), residues: 1994 helix: -0.69 (0.15), residues: 1004 sheet: -1.96 (0.43), residues: 114 loop : -3.52 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 609 HIS 0.008 0.002 HIS A 336 PHE 0.035 0.002 PHE A 453 TYR 0.026 0.002 TYR A 879 ARG 0.005 0.001 ARG A 670 *********************** 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 403 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 316 time to evaluate : 3.011 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: A 65 MET cc_start: 0.8425 (mmp) cc_final: 0.8029 (tpp) REVERT: A 76 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7876 (mt-10) REVERT: A 147 TRP cc_start: 0.8692 (m100) cc_final: 0.8301 (m100) REVERT: A 172 ASN cc_start: 0.8540 (t0) cc_final: 0.8226 (t0) REVERT: A 227 ASP cc_start: 0.9105 (p0) cc_final: 0.8829 (t70) REVERT: A 253 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8360 (p0) REVERT: A 295 LEU cc_start: 0.9010 (tp) cc_final: 0.8802 (tt) REVERT: A 315 GLU cc_start: 0.9373 (tt0) cc_final: 0.8923 (tm-30) REVERT: A 343 LYS cc_start: 0.9245 (mttt) cc_final: 0.8946 (mmtt) REVERT: A 376 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9186 (t) REVERT: A 422 PHE cc_start: 0.7197 (t80) cc_final: 0.6875 (t80) REVERT: A 460 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7731 (p0) REVERT: A 539 ARG cc_start: 0.9176 (ptm160) cc_final: 0.8859 (ttp80) REVERT: A 568 LYS cc_start: 0.8782 (mttm) cc_final: 0.8040 (tttt) REVERT: A 576 LEU cc_start: 0.9142 (tp) cc_final: 0.8607 (tt) REVERT: A 656 MET cc_start: 0.9073 (mtm) cc_final: 0.8487 (mtm) REVERT: A 768 MET cc_start: 0.8368 (ptp) cc_final: 0.8059 (ptp) REVERT: A 851 ASP cc_start: 0.9034 (t0) cc_final: 0.8789 (t70) REVERT: A 856 GLN cc_start: 0.8688 (pt0) cc_final: 0.8468 (pm20) REVERT: A 865 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8123 (pt) REVERT: A 959 MET cc_start: 0.7898 (mpp) cc_final: 0.7676 (mpp) REVERT: A 968 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8772 (mm-30) REVERT: A 1007 ASN cc_start: 0.7944 (p0) cc_final: 0.7596 (m-40) REVERT: A 1031 SER cc_start: 0.9315 (t) cc_final: 0.9044 (p) REVERT: A 1077 LYS cc_start: 0.9113 (mttt) cc_final: 0.8741 (mmtp) REVERT: A 1137 ASP cc_start: 0.9125 (t0) cc_final: 0.8694 (t0) REVERT: A 1141 ASP cc_start: 0.8936 (t0) cc_final: 0.8702 (t70) REVERT: A 1228 ARG cc_start: 0.7000 (ttt180) cc_final: 0.6492 (tpt170) REVERT: A 1241 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.8888 (p) REVERT: A 1308 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7879 (mt-10) REVERT: A 1398 ARG cc_start: 0.8306 (ptt180) cc_final: 0.7946 (mtt180) REVERT: A 1419 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7654 (ttt90) REVERT: A 1442 LYS cc_start: 0.8684 (tptt) cc_final: 0.8425 (ttmt) REVERT: A 1507 LEU cc_start: 0.9092 (mt) cc_final: 0.7674 (pt) REVERT: A 1512 ASP cc_start: 0.5222 (m-30) cc_final: 0.4608 (t70) REVERT: A 1626 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7540 (mp0) REVERT: A 1631 ILE cc_start: 0.7263 (mt) cc_final: 0.6958 (mm) REVERT: A 1663 TYR cc_start: 0.9140 (p90) cc_final: 0.8899 (p90) REVERT: A 1666 PHE cc_start: 0.8741 (p90) cc_final: 0.8512 (p90) REVERT: A 1668 SER cc_start: 0.9353 (t) cc_final: 0.9012 (t) REVERT: A 1691 PHE cc_start: 0.9286 (t80) cc_final: 0.9043 (t80) REVERT: A 1762 ASP cc_start: 0.7899 (m-30) cc_final: 0.6966 (m-30) REVERT: A 1763 MET cc_start: 0.8834 (mmm) cc_final: 0.8333 (tpt) REVERT: A 1789 GLN cc_start: 0.7879 (pm20) cc_final: 0.7548 (tm-30) REVERT: A 1800 TYR cc_start: 0.7811 (t80) cc_final: 0.7357 (t80) REVERT: A 2046 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8009 (tp-100) REVERT: A 2074 ARG cc_start: 0.7667 (tpt90) cc_final: 0.7293 (ttm-80) REVERT: A 2095 LEU cc_start: 0.8358 (tp) cc_final: 0.8120 (tt) outliers start: 87 outliers final: 55 residues processed: 387 average time/residue: 0.6758 time to fit residues: 389.1612 Evaluate side-chains 355 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 294 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 149 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 223 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP 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 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 763 ASN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 805 ILE 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 905 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1003 LEU 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 1241 SER Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1419 ARG Chi-restraints excluded: chain A residue 1437 ILE Chi-restraints excluded: chain A residue 1464 THR Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1476 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 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 1687 SER Chi-restraints excluded: chain A residue 1736 LEU Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2053 ASN 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 179 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16456 Z= 0.288 Angle : 0.705 8.428 22270 Z= 0.381 Chirality : 0.042 0.167 2460 Planarity : 0.006 0.112 2828 Dihedral : 8.088 63.459 2231 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.74 % Favored : 85.11 % Rotamer: Outliers : 4.68 % Allowed : 19.45 % 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: -2.52 (0.18), residues: 1994 helix: -0.25 (0.16), residues: 1008 sheet: -2.06 (0.43), residues: 126 loop : -3.46 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 609 HIS 0.007 0.001 HIS A1105 PHE 0.021 0.002 PHE A 219 TYR 0.020 0.002 TYR A 879 ARG 0.004 0.000 ARG A 670 *********************** 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 399 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 315 time to evaluate : 3.113 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 76 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7774 (mt-10) REVERT: A 147 TRP cc_start: 0.8654 (m100) cc_final: 0.8268 (m100) REVERT: A 172 ASN cc_start: 0.8494 (t0) cc_final: 0.8091 (t0) REVERT: A 210 THR cc_start: 0.9245 (m) cc_final: 0.8887 (t) REVERT: A 227 ASP cc_start: 0.9110 (p0) cc_final: 0.8810 (t70) REVERT: A 253 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8355 (p0) REVERT: A 324 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7549 (tm-30) REVERT: A 342 VAL cc_start: 0.9159 (t) cc_final: 0.8890 (p) REVERT: A 343 LYS cc_start: 0.9239 (mttt) cc_final: 0.8921 (mmtm) REVERT: A 422 PHE cc_start: 0.6928 (t80) cc_final: 0.6622 (t80) REVERT: A 460 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7861 (p0) REVERT: A 512 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8014 (pt0) REVERT: A 539 ARG cc_start: 0.9121 (ptm160) cc_final: 0.8837 (ttp80) REVERT: A 568 LYS cc_start: 0.8777 (mttm) cc_final: 0.8059 (tttt) REVERT: A 576 LEU cc_start: 0.9137 (tp) cc_final: 0.8610 (tt) REVERT: A 622 PHE cc_start: 0.8840 (m-10) cc_final: 0.8567 (m-10) REVERT: A 656 MET cc_start: 0.9089 (mtm) cc_final: 0.8533 (mtm) REVERT: A 715 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8512 (p0) REVERT: A 802 ASN cc_start: 0.8399 (p0) cc_final: 0.7813 (p0) REVERT: A 851 ASP cc_start: 0.9025 (t0) cc_final: 0.8815 (t70) REVERT: A 856 GLN cc_start: 0.8703 (pt0) cc_final: 0.8420 (pm20) REVERT: A 865 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7818 (pt) REVERT: A 949 ASP cc_start: 0.8832 (m-30) cc_final: 0.8278 (t0) REVERT: A 1000 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8033 (tpp80) REVERT: A 1031 SER cc_start: 0.9321 (t) cc_final: 0.9079 (p) REVERT: A 1062 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7908 (t) REVERT: A 1077 LYS cc_start: 0.9083 (mttt) cc_final: 0.8721 (mmtp) REVERT: A 1137 ASP cc_start: 0.9095 (t0) cc_final: 0.8700 (t0) REVERT: A 1215 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6921 (mtm-85) REVERT: A 1228 ARG cc_start: 0.6899 (ttt180) cc_final: 0.6438 (tpt170) REVERT: A 1241 SER cc_start: 0.9397 (t) cc_final: 0.8822 (p) REVERT: A 1308 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 1398 ARG cc_start: 0.8357 (ptt180) cc_final: 0.8037 (mtt-85) REVERT: A 1478 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.8068 (ttp-170) REVERT: A 1507 LEU cc_start: 0.8986 (mt) cc_final: 0.7601 (pp) REVERT: A 1512 ASP cc_start: 0.5304 (m-30) cc_final: 0.4697 (t70) REVERT: A 1626 GLU cc_start: 0.8566 (mt-10) cc_final: 0.7449 (mp0) REVERT: A 1668 SER cc_start: 0.9237 (t) cc_final: 0.8950 (t) REVERT: A 1676 MET cc_start: 0.8923 (mtp) cc_final: 0.8504 (mtm) REVERT: A 1762 ASP cc_start: 0.7545 (OUTLIER) cc_final: 0.6754 (m-30) REVERT: A 1789 GLN cc_start: 0.7762 (pm20) cc_final: 0.7523 (tm-30) REVERT: A 1800 TYR cc_start: 0.7821 (t80) cc_final: 0.7385 (t80) REVERT: A 1807 ASN cc_start: 0.8641 (m-40) cc_final: 0.7904 (t0) REVERT: A 2080 ILE cc_start: 0.8392 (mm) cc_final: 0.7958 (pt) REVERT: A 2086 ARG cc_start: 0.7329 (ptm-80) cc_final: 0.6786 (pmt-80) REVERT: A 2095 LEU cc_start: 0.8296 (tp) cc_final: 0.8033 (tt) outliers start: 84 outliers final: 64 residues processed: 375 average time/residue: 0.6853 time to fit residues: 377.7692 Evaluate side-chains 362 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 291 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 253 ASP 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 346 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 715 ASN Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 827 GLU 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 905 THR Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1125 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 1464 THR Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER 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 1496 GLU Chi-restraints excluded: chain A residue 1511 SER 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 1736 LEU 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 1974 TRP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2053 ASN Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16456 Z= 0.253 Angle : 0.673 7.884 22270 Z= 0.362 Chirality : 0.041 0.161 2460 Planarity : 0.005 0.112 2828 Dihedral : 7.691 60.670 2225 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 1.15 % Allowed : 14.44 % Favored : 84.40 % Rotamer: Outliers : 5.07 % Allowed : 19.40 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.16 % 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: -2.20 (0.18), residues: 1994 helix: 0.02 (0.16), residues: 1010 sheet: -1.95 (0.43), residues: 127 loop : -3.33 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 609 HIS 0.006 0.001 HIS A 603 PHE 0.030 0.002 PHE A 453 TYR 0.018 0.002 TYR A 879 ARG 0.004 0.000 ARG A1454 *********************** 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 403 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 312 time to evaluate : 2.844 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: A 76 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7631 (mt-10) REVERT: A 147 TRP cc_start: 0.8613 (m100) cc_final: 0.8274 (m100) REVERT: A 172 ASN cc_start: 0.8433 (t0) cc_final: 0.8004 (t0) REVERT: A 210 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8874 (t) REVERT: A 227 ASP cc_start: 0.9091 (p0) cc_final: 0.8834 (t70) REVERT: A 253 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8375 (p0) REVERT: A 256 PHE cc_start: 0.8934 (m-80) cc_final: 0.8723 (m-10) REVERT: A 288 MET cc_start: 0.8426 (tpp) cc_final: 0.7856 (ttm) REVERT: A 324 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7572 (tm-30) REVERT: A 342 VAL cc_start: 0.9218 (t) cc_final: 0.8961 (p) REVERT: A 343 LYS cc_start: 0.9226 (mttt) cc_final: 0.8915 (mmtt) REVERT: A 422 PHE cc_start: 0.6826 (t80) cc_final: 0.6601 (t80) REVERT: A 460 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7906 (p0) REVERT: A 512 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7978 (pt0) REVERT: A 539 ARG cc_start: 0.9124 (ptm160) cc_final: 0.8913 (ttp80) REVERT: A 568 LYS cc_start: 0.8763 (mttm) cc_final: 0.8073 (tttp) REVERT: A 576 LEU cc_start: 0.9079 (tp) cc_final: 0.8497 (tt) REVERT: A 622 PHE cc_start: 0.8836 (m-10) cc_final: 0.8515 (m-10) REVERT: A 656 MET cc_start: 0.9077 (mtm) cc_final: 0.8622 (mtm) REVERT: A 805 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8721 (pt) REVERT: A 865 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7780 (pt) REVERT: A 949 ASP cc_start: 0.8717 (m-30) cc_final: 0.8129 (t0) REVERT: A 1000 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (tpp80) REVERT: A 1031 SER cc_start: 0.9319 (t) cc_final: 0.9073 (p) REVERT: A 1034 GLN cc_start: 0.7497 (tt0) cc_final: 0.7074 (tp40) REVERT: A 1062 SER cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (t) REVERT: A 1077 LYS cc_start: 0.9019 (mttt) cc_final: 0.8605 (mmtp) REVERT: A 1113 GLN cc_start: 0.9046 (pm20) cc_final: 0.8681 (pm20) REVERT: A 1137 ASP cc_start: 0.9092 (t0) cc_final: 0.8680 (t0) REVERT: A 1215 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6970 (mtm-85) REVERT: A 1228 ARG cc_start: 0.6911 (ttt180) cc_final: 0.6421 (tpt170) REVERT: A 1308 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 1315 MET cc_start: 0.6545 (ttt) cc_final: 0.6317 (mmp) REVERT: A 1398 ARG cc_start: 0.8312 (ptt180) cc_final: 0.7994 (mtt180) REVERT: A 1427 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7432 (mtp180) REVERT: A 1478 ARG cc_start: 0.8487 (tpp-160) cc_final: 0.8059 (ttp-170) REVERT: A 1507 LEU cc_start: 0.9040 (mt) cc_final: 0.7747 (pt) REVERT: A 1512 ASP cc_start: 0.5279 (m-30) cc_final: 0.4684 (t70) REVERT: A 1626 GLU cc_start: 0.8628 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 1762 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6532 (m-30) REVERT: A 1763 MET cc_start: 0.8652 (mmm) cc_final: 0.8279 (tpt) REVERT: A 1800 TYR cc_start: 0.7919 (t80) cc_final: 0.7502 (t80) REVERT: A 1807 ASN cc_start: 0.8645 (m-40) cc_final: 0.7899 (t0) REVERT: A 1980 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7139 (tptm) REVERT: A 2080 ILE cc_start: 0.8502 (mm) cc_final: 0.7977 (pt) REVERT: A 2086 ARG cc_start: 0.7304 (ptm-80) cc_final: 0.6872 (pmt-80) outliers start: 91 outliers final: 73 residues processed: 378 average time/residue: 0.6962 time to fit residues: 390.4254 Evaluate side-chains 370 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 289 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 149 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 253 ASP Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 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 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 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 772 ASP Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL 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 891 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 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 1464 THR Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER 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 1496 GLU Chi-restraints excluded: chain A residue 1511 SER 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 1735 ASP Chi-restraints excluded: chain A residue 1762 ASP Chi-restraints excluded: chain A residue 1855 ILE Chi-restraints excluded: chain A residue 1882 PHE 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 2049 LEU Chi-restraints excluded: chain A residue 2053 ASN Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 193 optimal weight: 0.9990 chunk 160 optimal weight: 0.0970 chunk 89 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- 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 ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2045 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16456 Z= 0.227 Angle : 0.656 7.638 22270 Z= 0.351 Chirality : 0.040 0.152 2460 Planarity : 0.005 0.113 2828 Dihedral : 7.470 59.278 2225 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.14 % Favored : 85.81 % Rotamer: Outliers : 4.52 % Allowed : 20.96 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.16 % 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: -1.88 (0.19), residues: 1994 helix: 0.30 (0.16), residues: 1014 sheet: -1.69 (0.41), residues: 138 loop : -3.24 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 609 HIS 0.006 0.001 HIS A 603 PHE 0.031 0.002 PHE A1691 TYR 0.020 0.001 TYR A1295 ARG 0.003 0.000 ARG A 684 *********************** 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 383 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 302 time to evaluate : 2.783 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: A 71 TRP cc_start: 0.8607 (m-10) cc_final: 0.7769 (m-90) REVERT: A 76 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7594 (mt-10) REVERT: A 147 TRP cc_start: 0.8566 (m100) cc_final: 0.8279 (m100) REVERT: A 172 ASN cc_start: 0.8497 (t0) cc_final: 0.8074 (t0) REVERT: A 227 ASP cc_start: 0.9062 (p0) cc_final: 0.8778 (t70) REVERT: A 256 PHE cc_start: 0.8850 (m-80) cc_final: 0.8523 (m-10) REVERT: A 310 GLN cc_start: 0.8424 (pm20) cc_final: 0.8071 (pm20) REVERT: A 324 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7563 (tm-30) REVERT: A 342 VAL cc_start: 0.9195 (t) cc_final: 0.8929 (p) REVERT: A 343 LYS cc_start: 0.9212 (mttt) cc_final: 0.8890 (mmtt) REVERT: A 422 PHE cc_start: 0.6735 (t80) cc_final: 0.6507 (t80) REVERT: A 460 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 512 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8057 (pt0) REVERT: A 539 ARG cc_start: 0.9096 (ptm160) cc_final: 0.8789 (ttp80) REVERT: A 568 LYS cc_start: 0.8658 (mttm) cc_final: 0.8037 (tttp) REVERT: A 576 LEU cc_start: 0.9015 (tp) cc_final: 0.8488 (tt) REVERT: A 592 LEU cc_start: 0.4160 (OUTLIER) cc_final: 0.3946 (mt) REVERT: A 656 MET cc_start: 0.9062 (mtm) cc_final: 0.8599 (mtm) REVERT: A 748 MET cc_start: 0.8850 (tpp) cc_final: 0.8590 (tpp) REVERT: A 805 ILE cc_start: 0.8937 (pt) cc_final: 0.8706 (pt) REVERT: A 865 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7509 (pt) REVERT: A 912 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8407 (tpt170) REVERT: A 949 ASP cc_start: 0.8722 (m-30) cc_final: 0.8171 (t0) REVERT: A 1000 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8180 (tpp80) REVERT: A 1031 SER cc_start: 0.9299 (t) cc_final: 0.9055 (p) REVERT: A 1034 GLN cc_start: 0.7453 (tt0) cc_final: 0.7142 (tp40) REVERT: A 1037 ARG cc_start: 0.8166 (mmp80) cc_final: 0.7939 (mpp-170) REVERT: A 1077 LYS cc_start: 0.8989 (mttt) cc_final: 0.8565 (mmtp) REVERT: A 1215 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7095 (mtm-85) REVERT: A 1228 ARG cc_start: 0.6874 (ttt180) cc_final: 0.6440 (tpt170) REVERT: A 1308 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 1315 MET cc_start: 0.6576 (ttt) cc_final: 0.6336 (mmp) REVERT: A 1398 ARG cc_start: 0.8264 (ptt180) cc_final: 0.7804 (ttt180) REVERT: A 1478 ARG cc_start: 0.8463 (tpp-160) cc_final: 0.8019 (ttp-170) REVERT: A 1507 LEU cc_start: 0.9045 (mt) cc_final: 0.7765 (pt) REVERT: A 1512 ASP cc_start: 0.5298 (m-30) cc_final: 0.4683 (t70) REVERT: A 1626 GLU cc_start: 0.8638 (mt-10) cc_final: 0.7546 (mp0) REVERT: A 1627 MET cc_start: 0.9033 (tpp) cc_final: 0.8739 (tpt) REVERT: A 1762 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: A 1763 MET cc_start: 0.8556 (mmm) cc_final: 0.8211 (tpt) REVERT: A 1800 TYR cc_start: 0.7864 (t80) cc_final: 0.7584 (t80) REVERT: A 1807 ASN cc_start: 0.8644 (m-40) cc_final: 0.7915 (t0) REVERT: A 2080 ILE cc_start: 0.8461 (mm) cc_final: 0.8014 (pt) REVERT: A 2086 ARG cc_start: 0.7172 (ptm-80) cc_final: 0.6689 (pmt-80) REVERT: A 2095 LEU cc_start: 0.8310 (tp) cc_final: 0.8046 (tt) outliers start: 81 outliers final: 66 residues processed: 360 average time/residue: 0.6809 time to fit residues: 363.2265 Evaluate side-chains 353 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 281 time to evaluate : 2.879 ------------------------------------------------------------------------------- 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 116 VAL 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 318 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 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 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 603 HIS Chi-restraints excluded: chain A residue 609 TRP Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 1000 ARG 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 1125 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 1440 ILE Chi-restraints excluded: chain A residue 1464 THR 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 1496 GLU Chi-restraints excluded: chain A residue 1511 SER 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 1687 SER 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 1882 PHE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1973 PHE Chi-restraints excluded: chain A residue 1974 TRP Chi-restraints excluded: chain A residue 2029 SER Chi-restraints excluded: chain A residue 2049 LEU Chi-restraints excluded: chain A residue 2053 ASN Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16456 Z= 0.309 Angle : 0.687 7.789 22270 Z= 0.371 Chirality : 0.041 0.149 2460 Planarity : 0.006 0.113 2828 Dihedral : 7.291 58.104 2218 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 1.10 % Allowed : 14.14 % Favored : 84.75 % Rotamer: Outliers : 5.07 % Allowed : 20.35 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.16 % 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: -1.92 (0.18), residues: 1994 helix: 0.27 (0.16), residues: 1015 sheet: -1.69 (0.43), residues: 137 loop : -3.28 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 609 HIS 0.007 0.001 HIS A 603 PHE 0.033 0.002 PHE A1691 TYR 0.018 0.002 TYR A2009 ARG 0.004 0.000 ARG A1454 *********************** 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 371 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 280 time to evaluate : 2.817 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: A 76 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7555 (mt-10) REVERT: A 147 TRP cc_start: 0.8502 (m100) cc_final: 0.8251 (m100) REVERT: A 172 ASN cc_start: 0.8443 (t0) cc_final: 0.7972 (t0) REVERT: A 210 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8887 (t) REVERT: A 227 ASP cc_start: 0.9071 (p0) cc_final: 0.8838 (t70) REVERT: A 288 MET cc_start: 0.8330 (tpp) cc_final: 0.7804 (ttm) REVERT: A 324 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7596 (tm-30) REVERT: A 342 VAL cc_start: 0.9253 (t) cc_final: 0.8960 (p) REVERT: A 343 LYS cc_start: 0.9210 (mttt) cc_final: 0.8854 (mmtt) REVERT: A 422 PHE cc_start: 0.6760 (t80) cc_final: 0.6514 (t80) REVERT: A 460 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7856 (p0) REVERT: A 512 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8038 (pt0) REVERT: A 539 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8829 (ttp80) REVERT: A 568 LYS cc_start: 0.8800 (mttm) cc_final: 0.8200 (tttt) REVERT: A 576 LEU cc_start: 0.9018 (tp) cc_final: 0.8410 (tt) REVERT: A 592 LEU cc_start: 0.4092 (OUTLIER) cc_final: 0.3866 (mt) REVERT: A 656 MET cc_start: 0.9068 (mtm) cc_final: 0.8582 (mtm) REVERT: A 805 ILE cc_start: 0.8925 (pt) cc_final: 0.8709 (pt) REVERT: A 865 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7759 (pt) REVERT: A 912 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8446 (tpt170) REVERT: A 949 ASP cc_start: 0.8730 (m-30) cc_final: 0.8170 (t0) REVERT: A 1000 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8190 (tpp80) REVERT: A 1031 SER cc_start: 0.9328 (t) cc_final: 0.9072 (p) REVERT: A 1034 GLN cc_start: 0.7460 (tt0) cc_final: 0.7171 (tp40) REVERT: A 1037 ARG cc_start: 0.8220 (mmp80) cc_final: 0.7988 (mpp-170) REVERT: A 1062 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 1077 LYS cc_start: 0.8982 (mttt) cc_final: 0.8628 (mptt) REVERT: A 1228 ARG cc_start: 0.6892 (ttt180) cc_final: 0.6455 (tpt170) REVERT: A 1241 SER cc_start: 0.9380 (t) cc_final: 0.8758 (p) REVERT: A 1308 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 1315 MET cc_start: 0.6781 (ttt) cc_final: 0.6532 (mmp) REVERT: A 1329 TRP cc_start: 0.7680 (t60) cc_final: 0.7457 (t60) REVERT: A 1426 LYS cc_start: 0.7425 (mttt) cc_final: 0.6802 (pttp) REVERT: A 1478 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.8092 (ttp-170) REVERT: A 1507 LEU cc_start: 0.9042 (mt) cc_final: 0.7788 (pt) REVERT: A 1512 ASP cc_start: 0.5328 (m-30) cc_final: 0.4706 (t70) REVERT: A 1546 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7711 (tpp80) REVERT: A 1626 GLU cc_start: 0.8693 (mt-10) cc_final: 0.7597 (mp0) REVERT: A 1627 MET cc_start: 0.8984 (tpp) cc_final: 0.8714 (tpt) REVERT: A 1762 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6511 (m-30) REVERT: A 1763 MET cc_start: 0.8585 (mmm) cc_final: 0.8240 (tpt) REVERT: A 1800 TYR cc_start: 0.8004 (t80) cc_final: 0.7780 (t80) REVERT: A 1980 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7246 (tptm) REVERT: A 2030 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7507 (mp) REVERT: A 2045 ASN cc_start: 0.9011 (t0) cc_final: 0.8809 (t0) REVERT: A 2086 ARG cc_start: 0.7186 (ptm-80) cc_final: 0.6696 (pmt-80) outliers start: 91 outliers final: 75 residues processed: 346 average time/residue: 0.6572 time to fit residues: 337.5563 Evaluate side-chains 351 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 267 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER 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 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 290 GLU 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 452 CYS 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 720 THR Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 851 ASP 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 912 ARG Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 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 1472 SER Chi-restraints excluded: chain A residue 1482 VAL Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1511 SER 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 1694 LEU 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 1882 PHE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1894 ASP Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1973 PHE 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 2053 ASN Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16456 Z= 0.273 Angle : 0.674 7.531 22270 Z= 0.362 Chirality : 0.041 0.149 2460 Planarity : 0.006 0.114 2828 Dihedral : 7.220 56.850 2217 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 1.15 % Allowed : 13.94 % Favored : 84.90 % Rotamer: Outliers : 5.02 % Allowed : 21.52 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.17 % Twisted General : 0.16 % 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: -1.83 (0.19), residues: 1994 helix: 0.35 (0.16), residues: 1017 sheet: -1.60 (0.44), residues: 137 loop : -3.24 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 609 HIS 0.007 0.001 HIS A 603 PHE 0.040 0.002 PHE A1691 TYR 0.017 0.002 TYR A2009 ARG 0.003 0.000 ARG A 670 *********************** 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 370 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 280 time to evaluate : 2.669 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: A 76 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7543 (mt-10) REVERT: A 172 ASN cc_start: 0.8381 (t0) cc_final: 0.7873 (t0) REVERT: A 210 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8894 (t) REVERT: A 227 ASP cc_start: 0.9013 (p0) cc_final: 0.8774 (t70) REVERT: A 253 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8269 (p0) REVERT: A 288 MET cc_start: 0.8285 (tpp) cc_final: 0.7788 (ttm) REVERT: A 324 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7583 (tm-30) REVERT: A 342 VAL cc_start: 0.9243 (t) cc_final: 0.8958 (p) REVERT: A 343 LYS cc_start: 0.9212 (mttt) cc_final: 0.8891 (mmtt) REVERT: A 460 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7863 (p0) REVERT: A 512 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7976 (pt0) REVERT: A 539 ARG cc_start: 0.9092 (ptm160) cc_final: 0.8794 (ttp80) REVERT: A 568 LYS cc_start: 0.8705 (mttm) cc_final: 0.8137 (tttt) REVERT: A 576 LEU cc_start: 0.8968 (tp) cc_final: 0.8367 (tt) REVERT: A 592 LEU cc_start: 0.4151 (OUTLIER) cc_final: 0.3933 (mt) REVERT: A 656 MET cc_start: 0.9076 (mtm) cc_final: 0.8575 (mtm) REVERT: A 805 ILE cc_start: 0.8912 (pt) cc_final: 0.8705 (pt) REVERT: A 865 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7634 (pt) REVERT: A 912 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8428 (tpt170) REVERT: A 949 ASP cc_start: 0.8670 (m-30) cc_final: 0.8122 (t0) REVERT: A 1000 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (tpp80) REVERT: A 1031 SER cc_start: 0.9317 (t) cc_final: 0.9054 (p) REVERT: A 1034 GLN cc_start: 0.7451 (tt0) cc_final: 0.7020 (tp40) REVERT: A 1062 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8403 (t) REVERT: A 1077 LYS cc_start: 0.8976 (mttt) cc_final: 0.8634 (mptt) REVERT: A 1228 ARG cc_start: 0.6906 (ttt180) cc_final: 0.6502 (tpt170) REVERT: A 1241 SER cc_start: 0.9377 (t) cc_final: 0.8764 (p) REVERT: A 1308 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 1329 TRP cc_start: 0.7652 (t60) cc_final: 0.7443 (t60) REVERT: A 1426 LYS cc_start: 0.7453 (mttt) cc_final: 0.6815 (pttp) REVERT: A 1478 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8071 (ttp-170) REVERT: A 1507 LEU cc_start: 0.9046 (mt) cc_final: 0.7872 (pt) REVERT: A 1512 ASP cc_start: 0.5573 (m-30) cc_final: 0.5068 (t70) REVERT: A 1626 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7610 (mp0) REVERT: A 1627 MET cc_start: 0.8951 (tpp) cc_final: 0.8693 (tpt) REVERT: A 1762 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: A 1763 MET cc_start: 0.8538 (mmm) cc_final: 0.8280 (tpt) REVERT: A 1800 TYR cc_start: 0.7983 (t80) cc_final: 0.7757 (t80) REVERT: A 1980 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7311 (tptm) REVERT: A 2030 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7609 (mp) outliers start: 90 outliers final: 76 residues processed: 346 average time/residue: 0.6526 time to fit residues: 337.7856 Evaluate side-chains 358 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 272 time to evaluate : 2.718 ------------------------------------------------------------------------------- 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 149 ASP Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 290 GLU 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 452 CYS 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 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 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 763 ASN Chi-restraints excluded: chain A residue 766 GLU Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 851 ASP 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 912 ARG 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 1043 PHE 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 1243 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 1464 THR Chi-restraints excluded: chain A residue 1467 HIS Chi-restraints excluded: chain A residue 1472 SER Chi-restraints excluded: chain A residue 1495 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1609 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 1636 LEU Chi-restraints excluded: chain A residue 1687 SER Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1711 SER 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 1882 PHE Chi-restraints excluded: chain A residue 1883 THR Chi-restraints excluded: chain A residue 1908 VAL Chi-restraints excluded: chain A residue 1973 PHE 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 2053 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.2980 chunk 168 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1643 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16456 Z= 0.221 Angle : 0.653 8.143 22270 Z= 0.348 Chirality : 0.040 0.149 2460 Planarity : 0.005 0.113 2828 Dihedral : 7.020 53.728 2215 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 1.05 % Allowed : 13.54 % Favored : 85.41 % Rotamer: Outliers : 4.46 % Allowed : 22.69 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -1.63 (0.19), residues: 1994 helix: 0.53 (0.16), residues: 1013 sheet: -1.54 (0.44), residues: 135 loop : -3.16 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 609 HIS 0.006 0.001 HIS A 603 PHE 0.047 0.002 PHE A1691 TYR 0.015 0.001 TYR A2009 ARG 0.003 0.000 ARG A 670 *********************** 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 375 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 295 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TRP cc_start: 0.8591 (m-10) cc_final: 0.7817 (m-90) REVERT: A 76 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7484 (mt-10) REVERT: A 172 ASN cc_start: 0.8386 (t0) cc_final: 0.7853 (t0) REVERT: A 227 ASP cc_start: 0.8984 (p0) cc_final: 0.8750 (t70) REVERT: A 253 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8364 (p0) REVERT: A 288 MET cc_start: 0.8114 (tpp) cc_final: 0.7591 (ttm) REVERT: A 324 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7534 (tm-30) REVERT: A 342 VAL cc_start: 0.9224 (t) cc_final: 0.8943 (p) REVERT: A 343 LYS cc_start: 0.9209 (mttt) cc_final: 0.8880 (mmtt) REVERT: A 460 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7868 (p0) REVERT: A 512 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7962 (pt0) REVERT: A 539 ARG cc_start: 0.9087 (ptm160) cc_final: 0.8792 (ttp80) REVERT: A 568 LYS cc_start: 0.8691 (mttm) cc_final: 0.8118 (tttt) REVERT: A 576 LEU cc_start: 0.8926 (tp) cc_final: 0.8345 (tt) REVERT: A 595 TYR cc_start: 0.8075 (m-80) cc_final: 0.7387 (m-80) REVERT: A 656 MET cc_start: 0.9027 (mtm) cc_final: 0.8493 (mtm) REVERT: A 805 ILE cc_start: 0.8879 (pt) cc_final: 0.8663 (pt) REVERT: A 865 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7520 (pt) REVERT: A 912 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8410 (tpt170) REVERT: A 949 ASP cc_start: 0.8604 (m-30) cc_final: 0.8075 (t0) REVERT: A 1000 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8176 (tpp80) REVERT: A 1031 SER cc_start: 0.9286 (t) cc_final: 0.9082 (m) REVERT: A 1034 GLN cc_start: 0.7413 (tt0) cc_final: 0.6987 (tp40) REVERT: A 1062 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8334 (t) REVERT: A 1077 LYS cc_start: 0.8945 (mttt) cc_final: 0.8611 (mptt) REVERT: A 1228 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6540 (tpt170) REVERT: A 1308 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8023 (mt-10) REVERT: A 1426 LYS cc_start: 0.7399 (mttt) cc_final: 0.6767 (pttp) REVERT: A 1478 ARG cc_start: 0.8523 (tpp-160) cc_final: 0.8066 (ttp-170) REVERT: A 1507 LEU cc_start: 0.9060 (mt) cc_final: 0.7911 (pt) REVERT: A 1512 ASP cc_start: 0.5528 (m-30) cc_final: 0.5083 (t70) REVERT: A 1546 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7750 (tpp80) REVERT: A 1626 GLU cc_start: 0.8704 (mt-10) cc_final: 0.7605 (mp0) REVERT: A 1627 MET cc_start: 0.8934 (tpp) cc_final: 0.8669 (tpt) REVERT: A 1762 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: A 1763 MET cc_start: 0.8471 (mmm) cc_final: 0.8249 (tpt) REVERT: A 1836 MET cc_start: 0.7355 (tmm) cc_final: 0.6862 (tmm) REVERT: A 2030 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7596 (mp) outliers start: 80 outliers final: 66 residues processed: 352 average time/residue: 0.6495 time to fit residues: 340.7574 Evaluate side-chains 354 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 280 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 253 ASP Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 318 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 452 CYS 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 524 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 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 763 ASN Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 851 ASP 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 1000 ARG 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 1125 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 1243 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 1496 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1553 SER 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 1687 SER Chi-restraints excluded: chain A residue 1711 SER 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 1882 PHE 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 2053 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 199 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16456 Z= 0.194 Angle : 0.642 9.217 22270 Z= 0.339 Chirality : 0.040 0.198 2460 Planarity : 0.005 0.113 2828 Dihedral : 6.678 47.171 2211 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.14 % Favored : 86.81 % Rotamer: Outliers : 3.57 % Allowed : 23.80 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -1.46 (0.19), residues: 1994 helix: 0.69 (0.16), residues: 1017 sheet: -1.36 (0.45), residues: 133 loop : -3.12 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 609 HIS 0.006 0.001 HIS A 603 PHE 0.032 0.001 PHE A1691 TYR 0.013 0.001 TYR A 879 ARG 0.005 0.000 ARG A1330 ********************** 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 370 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 306 time to evaluate : 2.132 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 71 TRP cc_start: 0.8551 (m-10) cc_final: 0.7791 (m-90) REVERT: A 76 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7430 (mt-10) REVERT: A 147 TRP cc_start: 0.8542 (m100) cc_final: 0.8269 (m100) REVERT: A 172 ASN cc_start: 0.8341 (t0) cc_final: 0.7779 (t0) REVERT: A 227 ASP cc_start: 0.9031 (p0) cc_final: 0.8829 (t70) REVERT: A 253 ASP cc_start: 0.8956 (m-30) cc_final: 0.8461 (p0) REVERT: A 288 MET cc_start: 0.7937 (tpp) cc_final: 0.7551 (ttm) REVERT: A 324 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7534 (tm-30) REVERT: A 342 VAL cc_start: 0.9068 (t) cc_final: 0.8782 (p) REVERT: A 512 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7996 (pt0) REVERT: A 539 ARG cc_start: 0.9068 (ptm160) cc_final: 0.8788 (ttp80) REVERT: A 568 LYS cc_start: 0.8651 (mttm) cc_final: 0.8118 (tttp) REVERT: A 595 TYR cc_start: 0.7944 (m-80) cc_final: 0.7217 (m-80) REVERT: A 628 PHE cc_start: 0.8959 (m-80) cc_final: 0.8623 (m-80) REVERT: A 656 MET cc_start: 0.8962 (mtm) cc_final: 0.8345 (mtm) REVERT: A 748 MET cc_start: 0.8871 (tpp) cc_final: 0.8587 (tpp) REVERT: A 805 ILE cc_start: 0.8847 (pt) cc_final: 0.8622 (pt) REVERT: A 865 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7359 (pt) REVERT: A 949 ASP cc_start: 0.8499 (m-30) cc_final: 0.7969 (t0) REVERT: A 1000 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (tpp80) REVERT: A 1034 GLN cc_start: 0.7308 (tt0) cc_final: 0.6931 (tp40) REVERT: A 1077 LYS cc_start: 0.8927 (mttt) cc_final: 0.8591 (mptt) REVERT: A 1165 GLN cc_start: 0.7100 (pp30) cc_final: 0.6746 (pp30) REVERT: A 1228 ARG cc_start: 0.7080 (ttt180) cc_final: 0.6618 (tpt170) REVERT: A 1251 MET cc_start: 0.8709 (ttp) cc_final: 0.8388 (ttp) REVERT: A 1308 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8095 (mt-10) REVERT: A 1315 MET cc_start: 0.6626 (ttt) cc_final: 0.6397 (mmp) REVERT: A 1478 ARG cc_start: 0.8523 (tpp-160) cc_final: 0.8072 (ttm-80) REVERT: A 1507 LEU cc_start: 0.9045 (mt) cc_final: 0.7933 (pt) REVERT: A 1512 ASP cc_start: 0.5608 (m-30) cc_final: 0.5233 (t70) REVERT: A 1546 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7727 (tpp80) REVERT: A 1626 GLU cc_start: 0.8741 (mt-10) cc_final: 0.7638 (mp0) REVERT: A 1627 MET cc_start: 0.8915 (tpp) cc_final: 0.8656 (tpt) REVERT: A 1800 TYR cc_start: 0.7505 (t80) cc_final: 0.6940 (t80) REVERT: A 1836 MET cc_start: 0.7442 (tmm) cc_final: 0.7037 (tmm) REVERT: A 1882 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 1996 PHE cc_start: 0.8234 (t80) cc_final: 0.7413 (t80) REVERT: A 2001 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 2045 ASN cc_start: 0.8817 (t0) cc_final: 0.8587 (p0) REVERT: A 2095 LEU cc_start: 0.8222 (tp) cc_final: 0.7924 (tt) outliers start: 64 outliers final: 55 residues processed: 349 average time/residue: 0.6545 time to fit residues: 339.5244 Evaluate side-chains 351 residues out of total 1794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 293 time to evaluate : 2.648 ------------------------------------------------------------------------------- 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 290 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 452 CYS 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 554 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 772 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 851 ASP Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 1000 ARG Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1057 ARG Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1125 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 1496 GLU Chi-restraints excluded: chain A residue 1511 SER Chi-restraints excluded: chain A residue 1553 SER Chi-restraints excluded: chain A residue 1609 ILE Chi-restraints excluded: chain A residue 1615 TYR Chi-restraints excluded: chain A residue 1633 ASN Chi-restraints excluded: chain A residue 1711 SER Chi-restraints excluded: chain A residue 1729 CYS Chi-restraints excluded: chain A residue 1735 ASP Chi-restraints excluded: chain A residue 1882 PHE 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 2049 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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** A1692 ASN ** A2035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.168245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.146130 restraints weight = 82396.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.152386 restraints weight = 35192.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.156201 restraints weight = 19537.074| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16456 Z= 0.206 Angle : 0.638 7.339 22270 Z= 0.338 Chirality : 0.040 0.162 2460 Planarity : 0.005 0.112 2828 Dihedral : 6.532 49.795 2208 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 1.00 % Allowed : 12.69 % Favored : 86.31 % Rotamer: Outliers : 3.62 % Allowed : 23.80 % Favored : 72.58 % 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: -1.43 (0.19), residues: 1994 helix: 0.71 (0.16), residues: 1020 sheet: -1.59 (0.47), residues: 121 loop : -3.06 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 609 HIS 0.007 0.001 HIS A 603 PHE 0.022 0.001 PHE A 256 TYR 0.014 0.001 TYR A2009 ARG 0.002 0.000 ARG A 670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7408.88 seconds wall clock time: 131 minutes 19.13 seconds (7879.13 seconds total)