Starting phenix.real_space_refine on Sat Aug 3 14:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xq8_38569/08_2024/8xq8_38569.cif" } resolution = 3.35 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 46 5.16 5 C 5423 2.51 5 N 1380 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 129": "OD1" <-> "OD2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 924": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1122": "OE1" <-> "OE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1160": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8319 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 32, 'TRANS': 1018} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8319 At special positions: 0 Unit cell: (78.84, 111.24, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 1 15.00 O 1469 8.00 N 1380 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1982 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 74.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.991A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.824A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.707A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.932A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.652A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 406 Processing helix chain 'A' and resid 406 through 412 Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.686A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.415A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.738A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.627A pdb=" N GLU A 621 " --> pdb=" O VAL A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.940A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.148A pdb=" N CYS A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 705 removed outlier: 4.028A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 754 removed outlier: 3.847A pdb=" N LEU A 754 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 795 through 858 removed outlier: 4.347A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 5.524A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.701A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 4.145A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 976 Processing helix chain 'A' and resid 1043 through 1050 removed outlier: 3.559A pdb=" N LYS A1050 " --> pdb=" O GLY A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix removed outlier: 3.785A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.587A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.867A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.500A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1034 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1010 " --> pdb=" O PHE A1032 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 3.531A pdb=" N TYR A1125 " --> pdb=" O VAL A1188 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A1188 " --> pdb=" O TYR A1125 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1189 " --> pdb=" O ASP A1144 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.590A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2003 1.33 - 1.46: 1873 1.46 - 1.58: 4518 1.58 - 1.70: 5 1.70 - 1.83: 83 Bond restraints: 8482 Sorted by residual: bond pdb=" O2P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.643 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 CMP A2001 " pdb=" C5 CMP A2001 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C6 CMP A2001 " pdb=" N6 CMP A2001 " ideal model delta sigma weight residual 1.355 1.452 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5 CMP A2001 " pdb=" C6 CMP A2001 " ideal model delta sigma weight residual 1.490 1.421 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O1P CMP A2001 " pdb=" P CMP A2001 " ideal model delta sigma weight residual 1.510 1.452 0.058 2.00e-02 2.50e+03 8.27e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 91.63 - 100.43: 10 100.43 - 109.23: 696 109.23 - 118.03: 5895 118.03 - 126.83: 4775 126.83 - 135.64: 130 Bond angle restraints: 11506 Sorted by residual: angle pdb=" CG1 ILE A 652 " pdb=" CB ILE A 652 " pdb=" CG2 ILE A 652 " ideal model delta sigma weight residual 110.70 91.63 19.07 3.00e+00 1.11e-01 4.04e+01 angle pdb=" CA MET A 565 " pdb=" CB MET A 565 " pdb=" CG MET A 565 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.37e+01 angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 123.56 -3.32 6.30e-01 2.52e+00 2.77e+01 angle pdb=" CA GLN A1106 " pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CB GLN A1106 " pdb=" CG GLN A1106 " pdb=" CD GLN A1106 " ideal model delta sigma weight residual 112.60 121.09 -8.49 1.70e+00 3.46e-01 2.49e+01 ... (remaining 11501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 4686 26.26 - 52.53: 347 52.53 - 78.79: 32 78.79 - 105.06: 7 105.06 - 131.32: 1 Dihedral angle restraints: 5073 sinusoidal: 2016 harmonic: 3057 Sorted by residual: dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR A1049 " pdb=" C THR A1049 " pdb=" N LYS A1050 " pdb=" CA LYS A1050 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 754 " pdb=" C LEU A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1148 0.073 - 0.145: 186 0.145 - 0.218: 38 0.218 - 0.290: 4 0.290 - 0.363: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB ILE A 652 " pdb=" CA ILE A 652 " pdb=" CG1 ILE A 652 " pdb=" CG2 ILE A 652 " both_signs ideal model delta sigma weight residual False 2.64 3.01 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB VAL A 116 " pdb=" CA VAL A 116 " pdb=" CG1 VAL A 116 " pdb=" CG2 VAL A 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.97 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1377 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 766 " 0.044 2.00e-02 2.50e+03 4.05e-02 2.87e+01 pdb=" CG PHE A 766 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 766 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 766 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 766 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 766 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 766 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1123 " -0.352 9.50e-02 1.11e+02 1.58e-01 1.64e+01 pdb=" NE ARG A1123 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A1123 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A1123 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A1123 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO A 276 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.042 5.00e-02 4.00e+02 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1782 2.78 - 3.31: 8007 3.31 - 3.84: 14026 3.84 - 4.37: 15109 4.37 - 4.90: 26778 Nonbonded interactions: 65702 Sorted by model distance: nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.255 3.040 nonbonded pdb=" O SER A 735 " pdb=" OG SER A 735 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU A 954 " pdb=" OH TYR A1066 " model vdw 2.280 3.040 nonbonded pdb=" O PHE A 680 " pdb=" OG1 THR A 683 " model vdw 2.302 3.040 nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.306 3.040 ... (remaining 65697 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.880 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 0.007 0.133 8482 Z= 0.404 Angle : 1.245 19.067 11506 Z= 0.646 Chirality : 0.061 0.363 1380 Planarity : 0.010 0.158 1415 Dihedral : 17.539 131.319 3091 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.77 % Allowed : 29.61 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.52 (0.22), residues: 1039 helix: -0.78 (0.16), residues: 755 sheet: -0.54 (0.69), residues: 50 loop : -1.26 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 427 HIS 0.024 0.002 HIS A1156 PHE 0.092 0.003 PHE A 766 TYR 0.045 0.002 TYR A 267 ARG 0.018 0.002 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 256 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8231 (p) cc_final: 0.8025 (m) REVERT: A 174 LEU cc_start: 0.8155 (tp) cc_final: 0.7821 (tp) REVERT: A 263 GLN cc_start: 0.7713 (mt0) cc_final: 0.7115 (mp10) REVERT: A 295 ASN cc_start: 0.8131 (t0) cc_final: 0.7609 (t0) REVERT: A 354 GLU cc_start: 0.7987 (tt0) cc_final: 0.7632 (tm-30) REVERT: A 621 GLU cc_start: 0.7384 (tp30) cc_final: 0.7176 (tp30) REVERT: A 671 MET cc_start: 0.7143 (mtt) cc_final: 0.6775 (mtt) REVERT: A 940 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7810 (ttm-80) REVERT: A 1008 LEU cc_start: 0.7198 (tt) cc_final: 0.6981 (tp) REVERT: A 1161 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7020 (pt) outliers start: 7 outliers final: 3 residues processed: 260 average time/residue: 0.2346 time to fit residues: 79.7918 Evaluate side-chains 248 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 244 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 44 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 292 HIS A 295 ASN A 624 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN A 955 ASN A1054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8482 Z= 0.202 Angle : 0.654 14.525 11506 Z= 0.331 Chirality : 0.041 0.213 1380 Planarity : 0.005 0.056 1415 Dihedral : 6.327 135.150 1139 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.31 % Allowed : 23.76 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.41 (0.25), residues: 1039 helix: 0.75 (0.18), residues: 752 sheet: -0.31 (0.68), residues: 48 loop : -0.86 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 635 HIS 0.005 0.001 HIS A 157 PHE 0.030 0.001 PHE A 766 TYR 0.019 0.001 TYR A 267 ARG 0.010 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 253 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8348 (p) cc_final: 0.7996 (m) REVERT: A 155 ASP cc_start: 0.7836 (t0) cc_final: 0.7561 (t0) REVERT: A 174 LEU cc_start: 0.8148 (tp) cc_final: 0.7722 (tp) REVERT: A 179 VAL cc_start: 0.8027 (t) cc_final: 0.7553 (p) REVERT: A 199 MET cc_start: 0.7533 (mpp) cc_final: 0.7317 (mpp) REVERT: A 250 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7590 (mttp) REVERT: A 258 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 295 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 337 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7207 (tm-30) REVERT: A 381 ASP cc_start: 0.7398 (m-30) cc_final: 0.7176 (m-30) REVERT: A 389 ILE cc_start: 0.8177 (mt) cc_final: 0.7939 (mm) REVERT: A 443 GLU cc_start: 0.7949 (tp30) cc_final: 0.7531 (tp30) REVERT: A 671 MET cc_start: 0.7144 (mtt) cc_final: 0.6830 (mtt) REVERT: A 678 MET cc_start: 0.6273 (tpp) cc_final: 0.6005 (mpp) REVERT: A 810 MET cc_start: 0.5734 (tmm) cc_final: 0.5534 (tmm) REVERT: A 853 ILE cc_start: 0.8719 (tt) cc_final: 0.8462 (tp) REVERT: A 969 LEU cc_start: 0.8510 (tp) cc_final: 0.8143 (tp) REVERT: A 972 PHE cc_start: 0.8390 (t80) cc_final: 0.8177 (t80) REVERT: A 1097 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7545 (ttp80) outliers start: 39 outliers final: 18 residues processed: 272 average time/residue: 0.2331 time to fit residues: 83.4463 Evaluate side-chains 263 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1077 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1114 GLN A1135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8482 Z= 0.224 Angle : 0.628 14.217 11506 Z= 0.319 Chirality : 0.042 0.193 1380 Planarity : 0.004 0.051 1415 Dihedral : 6.100 132.574 1135 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.54 % Allowed : 24.31 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.97 (0.25), residues: 1039 helix: 1.24 (0.19), residues: 750 sheet: -0.11 (0.72), residues: 48 loop : -0.93 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 635 HIS 0.003 0.001 HIS A 350 PHE 0.024 0.001 PHE A 766 TYR 0.020 0.001 TYR A 267 ARG 0.012 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 155 ASP cc_start: 0.7874 (t0) cc_final: 0.7517 (t0) REVERT: A 174 LEU cc_start: 0.8192 (tp) cc_final: 0.7891 (tp) REVERT: A 250 LYS cc_start: 0.8119 (mmmm) cc_final: 0.7760 (mttp) REVERT: A 258 THR cc_start: 0.7435 (OUTLIER) cc_final: 0.7204 (p) REVERT: A 337 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 383 MET cc_start: 0.6728 (mmm) cc_final: 0.6398 (mmm) REVERT: A 443 GLU cc_start: 0.7892 (tp30) cc_final: 0.7510 (tp30) REVERT: A 671 MET cc_start: 0.7146 (mtt) cc_final: 0.6900 (mtt) REVERT: A 678 MET cc_start: 0.6330 (tpp) cc_final: 0.6071 (mpp) REVERT: A 810 MET cc_start: 0.5790 (tmm) cc_final: 0.5443 (tmm) REVERT: A 853 ILE cc_start: 0.8815 (tt) cc_final: 0.8430 (tp) REVERT: A 931 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 943 ASN cc_start: 0.7390 (t0) cc_final: 0.7038 (t0) REVERT: A 954 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: A 968 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7960 (ttmm) REVERT: A 972 PHE cc_start: 0.8384 (t80) cc_final: 0.8150 (t80) REVERT: A 1008 LEU cc_start: 0.7553 (tt) cc_final: 0.7321 (tp) REVERT: A 1097 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7566 (ttp80) REVERT: A 1118 LYS cc_start: 0.6277 (tmtt) cc_final: 0.5779 (tmtt) outliers start: 32 outliers final: 18 residues processed: 266 average time/residue: 0.2363 time to fit residues: 82.6563 Evaluate side-chains 260 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 954 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 677 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8482 Z= 0.217 Angle : 0.623 14.017 11506 Z= 0.314 Chirality : 0.042 0.201 1380 Planarity : 0.004 0.046 1415 Dihedral : 6.032 133.245 1135 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.98 % Allowed : 24.86 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.23 (0.26), residues: 1039 helix: 1.44 (0.19), residues: 754 sheet: -0.11 (0.72), residues: 48 loop : -0.89 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 419 HIS 0.005 0.001 HIS A 889 PHE 0.018 0.001 PHE A 766 TYR 0.021 0.001 TYR A 267 ARG 0.012 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 247 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7552 (mt) REVERT: A 116 VAL cc_start: 0.8335 (p) cc_final: 0.7984 (m) REVERT: A 155 ASP cc_start: 0.7908 (t0) cc_final: 0.7529 (t0) REVERT: A 174 LEU cc_start: 0.8231 (tp) cc_final: 0.7982 (tp) REVERT: A 199 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7445 (mpp) REVERT: A 217 LEU cc_start: 0.8819 (mm) cc_final: 0.8553 (mm) REVERT: A 250 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7981 (mttp) REVERT: A 258 THR cc_start: 0.7399 (OUTLIER) cc_final: 0.7157 (p) REVERT: A 295 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.7963 (t0) REVERT: A 337 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7020 (tm-30) REVERT: A 354 GLU cc_start: 0.8120 (tt0) cc_final: 0.7656 (tm-30) REVERT: A 383 MET cc_start: 0.6844 (mmm) cc_final: 0.6391 (mmm) REVERT: A 389 ILE cc_start: 0.8148 (mt) cc_final: 0.7898 (mm) REVERT: A 443 GLU cc_start: 0.7883 (tp30) cc_final: 0.7514 (tp30) REVERT: A 606 GLU cc_start: 0.7731 (tp30) cc_final: 0.7374 (tp30) REVERT: A 678 MET cc_start: 0.6342 (tpp) cc_final: 0.6085 (mpp) REVERT: A 746 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: A 810 MET cc_start: 0.5909 (tmm) cc_final: 0.5477 (tmm) REVERT: A 811 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.4973 (pp) REVERT: A 931 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 943 ASN cc_start: 0.7412 (t0) cc_final: 0.7001 (t0) REVERT: A 954 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 968 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7911 (ttmm) REVERT: A 1008 LEU cc_start: 0.7521 (tt) cc_final: 0.7303 (tp) REVERT: A 1097 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7543 (ttp80) REVERT: A 1116 LYS cc_start: 0.8020 (mtpm) cc_final: 0.7526 (mtpm) REVERT: A 1118 LYS cc_start: 0.6077 (tmtt) cc_final: 0.5190 (tmtt) REVERT: A 1190 ARG cc_start: 0.7345 (mpt180) cc_final: 0.6958 (mpt180) outliers start: 36 outliers final: 22 residues processed: 261 average time/residue: 0.2458 time to fit residues: 84.1383 Evaluate side-chains 271 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8482 Z= 0.208 Angle : 0.607 13.798 11506 Z= 0.308 Chirality : 0.041 0.187 1380 Planarity : 0.004 0.050 1415 Dihedral : 5.993 133.046 1135 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.53 % Allowed : 24.31 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.39 (0.26), residues: 1039 helix: 1.56 (0.19), residues: 754 sheet: -0.19 (0.72), residues: 48 loop : -0.84 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.009 0.001 HIS A 889 PHE 0.030 0.001 PHE A 766 TYR 0.021 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 155 ASP cc_start: 0.7947 (t0) cc_final: 0.7530 (t0) REVERT: A 174 LEU cc_start: 0.8245 (tp) cc_final: 0.8018 (tp) REVERT: A 199 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7578 (mmm) REVERT: A 250 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7985 (mttp) REVERT: A 258 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7122 (p) REVERT: A 295 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7908 (t0) REVERT: A 337 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 380 VAL cc_start: 0.8122 (m) cc_final: 0.7868 (t) REVERT: A 383 MET cc_start: 0.6892 (mmm) cc_final: 0.6459 (mmm) REVERT: A 443 GLU cc_start: 0.7881 (tp30) cc_final: 0.7509 (tp30) REVERT: A 647 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7963 (mmtm) REVERT: A 678 MET cc_start: 0.6350 (tpp) cc_final: 0.6102 (mpp) REVERT: A 810 MET cc_start: 0.5848 (tmm) cc_final: 0.5402 (tmm) REVERT: A 811 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5023 (pp) REVERT: A 845 ILE cc_start: 0.8433 (mt) cc_final: 0.8212 (mm) REVERT: A 888 GLU cc_start: 0.7843 (tp30) cc_final: 0.7623 (tp30) REVERT: A 943 ASN cc_start: 0.7431 (t0) cc_final: 0.7024 (t0) REVERT: A 954 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 989 VAL cc_start: 0.7734 (t) cc_final: 0.7530 (t) REVERT: A 1097 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7563 (ttp80) REVERT: A 1113 THR cc_start: 0.8452 (t) cc_final: 0.7898 (p) REVERT: A 1116 LYS cc_start: 0.8098 (mtpm) cc_final: 0.7547 (mtpm) REVERT: A 1118 LYS cc_start: 0.5834 (tmtt) cc_final: 0.4895 (mtmt) REVERT: A 1149 ASN cc_start: 0.6937 (p0) cc_final: 0.6702 (p0) REVERT: A 1190 ARG cc_start: 0.7327 (mpt180) cc_final: 0.6790 (mpt180) outliers start: 41 outliers final: 29 residues processed: 265 average time/residue: 0.2373 time to fit residues: 82.2878 Evaluate side-chains 273 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 239 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8482 Z= 0.281 Angle : 0.642 13.693 11506 Z= 0.327 Chirality : 0.042 0.180 1380 Planarity : 0.004 0.050 1415 Dihedral : 6.056 133.607 1135 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.64 % Allowed : 24.64 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.31 (0.26), residues: 1039 helix: 1.48 (0.19), residues: 756 sheet: -0.24 (0.72), residues: 48 loop : -0.79 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.009 0.001 HIS A 889 PHE 0.020 0.002 PHE A 766 TYR 0.021 0.002 TYR A 267 ARG 0.015 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 0.987 Fit side-chains REVERT: A 78 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7704 (mt) REVERT: A 155 ASP cc_start: 0.8021 (t0) cc_final: 0.7617 (t0) REVERT: A 199 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: A 250 LYS cc_start: 0.8261 (mmmm) cc_final: 0.8046 (mttp) REVERT: A 258 THR cc_start: 0.7352 (OUTLIER) cc_final: 0.7102 (p) REVERT: A 295 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7987 (t0) REVERT: A 337 GLU cc_start: 0.7712 (tm-30) cc_final: 0.6882 (tm-30) REVERT: A 380 VAL cc_start: 0.8205 (m) cc_final: 0.7949 (t) REVERT: A 383 MET cc_start: 0.7158 (mmm) cc_final: 0.6672 (mmm) REVERT: A 389 ILE cc_start: 0.8162 (mt) cc_final: 0.7915 (mm) REVERT: A 404 SER cc_start: 0.8471 (p) cc_final: 0.8250 (p) REVERT: A 443 GLU cc_start: 0.7883 (tp30) cc_final: 0.7477 (tp30) REVERT: A 581 GLU cc_start: 0.7794 (tp30) cc_final: 0.7502 (tp30) REVERT: A 590 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7940 (mt-10) REVERT: A 606 GLU cc_start: 0.7692 (tp30) cc_final: 0.7420 (tp30) REVERT: A 609 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.8066 (ttm-80) REVERT: A 647 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8155 (mmtm) REVERT: A 678 MET cc_start: 0.6403 (tpp) cc_final: 0.6149 (mpp) REVERT: A 746 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: A 810 MET cc_start: 0.5965 (tmm) cc_final: 0.5542 (tmm) REVERT: A 811 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5111 (pp) REVERT: A 878 VAL cc_start: 0.8323 (t) cc_final: 0.8119 (t) REVERT: A 888 GLU cc_start: 0.7880 (tp30) cc_final: 0.7603 (tp30) REVERT: A 943 ASN cc_start: 0.7585 (t0) cc_final: 0.7271 (t0) REVERT: A 954 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 1097 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7488 (ttp80) REVERT: A 1113 THR cc_start: 0.8512 (t) cc_final: 0.8004 (p) REVERT: A 1116 LYS cc_start: 0.8121 (mtpm) cc_final: 0.7595 (mtpm) REVERT: A 1118 LYS cc_start: 0.5835 (tmtt) cc_final: 0.4631 (tmtt) REVERT: A 1126 LEU cc_start: 0.8674 (mt) cc_final: 0.8458 (mp) REVERT: A 1190 ARG cc_start: 0.7298 (mpt180) cc_final: 0.6738 (mpt180) outliers start: 42 outliers final: 26 residues processed: 265 average time/residue: 0.2357 time to fit residues: 81.7451 Evaluate side-chains 278 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8482 Z= 0.215 Angle : 0.628 13.786 11506 Z= 0.319 Chirality : 0.041 0.170 1380 Planarity : 0.004 0.058 1415 Dihedral : 5.995 132.578 1135 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.75 % Allowed : 25.30 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.42 (0.26), residues: 1039 helix: 1.57 (0.19), residues: 755 sheet: -0.25 (0.73), residues: 48 loop : -0.76 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.007 0.001 HIS A 889 PHE 0.023 0.001 PHE A 766 TYR 0.021 0.001 TYR A 267 ARG 0.012 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 0.933 Fit side-chains REVERT: A 78 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 116 VAL cc_start: 0.8420 (p) cc_final: 0.8207 (p) REVERT: A 155 ASP cc_start: 0.8008 (t0) cc_final: 0.7597 (t0) REVERT: A 174 LEU cc_start: 0.8226 (tp) cc_final: 0.7958 (tp) REVERT: A 250 LYS cc_start: 0.8291 (mmmm) cc_final: 0.8045 (mtmm) REVERT: A 258 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.7119 (p) REVERT: A 337 GLU cc_start: 0.7699 (tm-30) cc_final: 0.6980 (tm-30) REVERT: A 380 VAL cc_start: 0.8224 (m) cc_final: 0.7993 (t) REVERT: A 383 MET cc_start: 0.7120 (mmm) cc_final: 0.6630 (mmm) REVERT: A 389 ILE cc_start: 0.8166 (mt) cc_final: 0.7923 (mm) REVERT: A 443 GLU cc_start: 0.7872 (tp30) cc_final: 0.7491 (tp30) REVERT: A 581 GLU cc_start: 0.7753 (tp30) cc_final: 0.7436 (tp30) REVERT: A 590 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 606 GLU cc_start: 0.7675 (tp30) cc_final: 0.7371 (tp30) REVERT: A 609 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.8022 (ttm-80) REVERT: A 678 MET cc_start: 0.6377 (tpp) cc_final: 0.6128 (mpp) REVERT: A 746 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: A 767 ASP cc_start: 0.7565 (m-30) cc_final: 0.7158 (p0) REVERT: A 810 MET cc_start: 0.5857 (tmm) cc_final: 0.5421 (tmm) REVERT: A 811 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5068 (pp) REVERT: A 888 GLU cc_start: 0.7858 (tp30) cc_final: 0.7594 (tp30) REVERT: A 931 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 943 ASN cc_start: 0.7505 (t0) cc_final: 0.7164 (t0) REVERT: A 1113 THR cc_start: 0.8511 (t) cc_final: 0.7987 (p) REVERT: A 1116 LYS cc_start: 0.8118 (mtpm) cc_final: 0.7577 (mtpm) REVERT: A 1118 LYS cc_start: 0.5930 (tmtt) cc_final: 0.4932 (mtmt) REVERT: A 1190 ARG cc_start: 0.7282 (mpt180) cc_final: 0.6584 (mpt180) outliers start: 43 outliers final: 32 residues processed: 259 average time/residue: 0.2457 time to fit residues: 83.9561 Evaluate side-chains 275 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1137 ASN Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 374 GLN A 691 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1156 HIS A1172 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8482 Z= 0.209 Angle : 0.637 13.762 11506 Z= 0.322 Chirality : 0.041 0.163 1380 Planarity : 0.004 0.061 1415 Dihedral : 5.968 132.226 1135 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.08 % Allowed : 25.19 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.46 (0.26), residues: 1039 helix: 1.60 (0.19), residues: 757 sheet: -0.24 (0.72), residues: 48 loop : -0.75 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.015 0.001 HIS A1156 PHE 0.046 0.002 PHE A 740 TYR 0.022 0.001 TYR A 267 ARG 0.011 0.001 ARG A1123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 244 time to evaluate : 0.924 Fit side-chains REVERT: A 78 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 116 VAL cc_start: 0.8416 (p) cc_final: 0.8199 (p) REVERT: A 155 ASP cc_start: 0.7999 (t0) cc_final: 0.7617 (t0) REVERT: A 174 LEU cc_start: 0.8247 (tp) cc_final: 0.7974 (tp) REVERT: A 250 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8046 (mtmm) REVERT: A 258 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7084 (p) REVERT: A 337 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 380 VAL cc_start: 0.8232 (m) cc_final: 0.8021 (t) REVERT: A 383 MET cc_start: 0.7140 (mmm) cc_final: 0.6641 (mmm) REVERT: A 389 ILE cc_start: 0.8171 (mt) cc_final: 0.7925 (mm) REVERT: A 443 GLU cc_start: 0.7869 (tp30) cc_final: 0.7491 (tp30) REVERT: A 581 GLU cc_start: 0.7821 (tp30) cc_final: 0.7524 (tp30) REVERT: A 590 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 606 GLU cc_start: 0.7673 (tp30) cc_final: 0.7350 (tp30) REVERT: A 609 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: A 678 MET cc_start: 0.6374 (tpp) cc_final: 0.6122 (mpp) REVERT: A 746 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: A 800 LYS cc_start: 0.8062 (pttt) cc_final: 0.7819 (pptt) REVERT: A 810 MET cc_start: 0.5845 (tmm) cc_final: 0.5406 (tmm) REVERT: A 811 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5119 (pp) REVERT: A 854 ILE cc_start: 0.8624 (tp) cc_final: 0.8409 (tt) REVERT: A 888 GLU cc_start: 0.7854 (tp30) cc_final: 0.7602 (tp30) REVERT: A 931 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 943 ASN cc_start: 0.7512 (t0) cc_final: 0.7169 (t0) REVERT: A 1113 THR cc_start: 0.8509 (t) cc_final: 0.7993 (p) REVERT: A 1116 LYS cc_start: 0.8115 (mtpm) cc_final: 0.7576 (mtpm) REVERT: A 1118 LYS cc_start: 0.5947 (tmtt) cc_final: 0.4960 (mtmt) REVERT: A 1190 ARG cc_start: 0.7294 (mpt180) cc_final: 0.6612 (mpt180) outliers start: 46 outliers final: 34 residues processed: 263 average time/residue: 0.2481 time to fit residues: 84.9330 Evaluate side-chains 280 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1137 ASN Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 96 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8482 Z= 0.220 Angle : 0.649 13.717 11506 Z= 0.328 Chirality : 0.041 0.166 1380 Planarity : 0.004 0.063 1415 Dihedral : 5.972 132.315 1135 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.53 % Allowed : 26.19 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.47 (0.26), residues: 1039 helix: 1.61 (0.19), residues: 759 sheet: -0.36 (0.70), residues: 48 loop : -0.74 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 419 HIS 0.023 0.001 HIS A1156 PHE 0.044 0.002 PHE A 740 TYR 0.021 0.001 TYR A 267 ARG 0.014 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 245 time to evaluate : 1.017 Fit side-chains REVERT: A 78 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 116 VAL cc_start: 0.8425 (p) cc_final: 0.8196 (p) REVERT: A 155 ASP cc_start: 0.8081 (t0) cc_final: 0.7712 (t0) REVERT: A 174 LEU cc_start: 0.8254 (tp) cc_final: 0.8036 (tp) REVERT: A 250 LYS cc_start: 0.8294 (mmmm) cc_final: 0.8051 (mtmm) REVERT: A 258 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.7070 (p) REVERT: A 295 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8021 (t0) REVERT: A 337 GLU cc_start: 0.7734 (tm-30) cc_final: 0.6937 (tm-30) REVERT: A 380 VAL cc_start: 0.8240 (m) cc_final: 0.8023 (t) REVERT: A 383 MET cc_start: 0.7169 (mmm) cc_final: 0.6668 (mmm) REVERT: A 389 ILE cc_start: 0.8170 (mt) cc_final: 0.7928 (mm) REVERT: A 443 GLU cc_start: 0.7868 (tp30) cc_final: 0.7487 (tp30) REVERT: A 581 GLU cc_start: 0.7822 (tp30) cc_final: 0.7500 (tp30) REVERT: A 606 GLU cc_start: 0.7669 (tp30) cc_final: 0.7332 (tp30) REVERT: A 609 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.7966 (ttm-80) REVERT: A 678 MET cc_start: 0.6362 (tpp) cc_final: 0.6102 (mpp) REVERT: A 746 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: A 767 ASP cc_start: 0.7503 (m-30) cc_final: 0.7127 (p0) REVERT: A 800 LYS cc_start: 0.8058 (pttt) cc_final: 0.7819 (pptt) REVERT: A 810 MET cc_start: 0.5892 (tmm) cc_final: 0.5440 (tmm) REVERT: A 811 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5117 (pp) REVERT: A 854 ILE cc_start: 0.8505 (tp) cc_final: 0.8296 (tt) REVERT: A 888 GLU cc_start: 0.7860 (tp30) cc_final: 0.7607 (tp30) REVERT: A 931 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 943 ASN cc_start: 0.7531 (t0) cc_final: 0.7191 (t0) REVERT: A 1113 THR cc_start: 0.8516 (t) cc_final: 0.8003 (p) REVERT: A 1116 LYS cc_start: 0.8145 (mtpm) cc_final: 0.7590 (mtpm) REVERT: A 1118 LYS cc_start: 0.5944 (tmtt) cc_final: 0.4967 (mtmt) REVERT: A 1185 ARG cc_start: 0.7234 (mtt-85) cc_final: 0.6965 (mmt90) REVERT: A 1188 VAL cc_start: 0.7926 (m) cc_final: 0.7705 (m) REVERT: A 1190 ARG cc_start: 0.7262 (mpt180) cc_final: 0.6654 (mpt180) outliers start: 41 outliers final: 34 residues processed: 260 average time/residue: 0.2359 time to fit residues: 80.2339 Evaluate side-chains 283 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 244 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 502 HIS Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.1980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8482 Z= 0.199 Angle : 0.649 13.774 11506 Z= 0.327 Chirality : 0.041 0.171 1380 Planarity : 0.004 0.063 1415 Dihedral : 5.968 132.097 1135 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.53 % Allowed : 25.86 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.53 (0.26), residues: 1039 helix: 1.64 (0.19), residues: 757 sheet: -0.22 (0.71), residues: 48 loop : -0.68 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.024 0.001 HIS A1156 PHE 0.042 0.002 PHE A 740 TYR 0.020 0.001 TYR A 267 ARG 0.013 0.001 ARG A 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 246 time to evaluate : 0.896 Fit side-chains REVERT: A 78 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7473 (mt) REVERT: A 116 VAL cc_start: 0.8419 (p) cc_final: 0.8189 (p) REVERT: A 155 ASP cc_start: 0.8033 (t0) cc_final: 0.7613 (t0) REVERT: A 174 LEU cc_start: 0.8240 (tp) cc_final: 0.7994 (tp) REVERT: A 250 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8067 (mtmm) REVERT: A 258 THR cc_start: 0.7284 (OUTLIER) cc_final: 0.7030 (p) REVERT: A 337 GLU cc_start: 0.7736 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 380 VAL cc_start: 0.8223 (m) cc_final: 0.8010 (t) REVERT: A 383 MET cc_start: 0.7151 (mmm) cc_final: 0.6646 (mmm) REVERT: A 389 ILE cc_start: 0.8183 (mt) cc_final: 0.7931 (mm) REVERT: A 443 GLU cc_start: 0.7863 (tp30) cc_final: 0.7485 (tp30) REVERT: A 581 GLU cc_start: 0.7805 (tp30) cc_final: 0.7486 (tp30) REVERT: A 606 GLU cc_start: 0.7675 (tp30) cc_final: 0.7331 (tp30) REVERT: A 609 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7960 (ttm-80) REVERT: A 678 MET cc_start: 0.6347 (tpp) cc_final: 0.6097 (mpp) REVERT: A 746 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: A 767 ASP cc_start: 0.7512 (m-30) cc_final: 0.7105 (p0) REVERT: A 800 LYS cc_start: 0.7995 (pttt) cc_final: 0.7761 (pptt) REVERT: A 810 MET cc_start: 0.5868 (tmm) cc_final: 0.5421 (tmm) REVERT: A 811 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5108 (pp) REVERT: A 888 GLU cc_start: 0.7854 (tp30) cc_final: 0.7591 (tp30) REVERT: A 931 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7884 (mm-30) REVERT: A 943 ASN cc_start: 0.7493 (t0) cc_final: 0.7152 (t0) REVERT: A 1033 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 1113 THR cc_start: 0.8517 (t) cc_final: 0.7983 (p) REVERT: A 1116 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7604 (mtpm) REVERT: A 1118 LYS cc_start: 0.5940 (tmtt) cc_final: 0.4967 (mtmt) REVERT: A 1122 GLU cc_start: 0.8008 (tp30) cc_final: 0.7702 (tp30) REVERT: A 1185 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6964 (mtt-85) REVERT: A 1188 VAL cc_start: 0.7903 (m) cc_final: 0.7656 (m) REVERT: A 1190 ARG cc_start: 0.7287 (mpt180) cc_final: 0.6604 (mpt180) REVERT: A 1191 ASN cc_start: 0.7534 (t0) cc_final: 0.7315 (m-40) outliers start: 41 outliers final: 34 residues processed: 263 average time/residue: 0.2314 time to fit residues: 79.4667 Evaluate side-chains 280 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 838 ASP Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1064 GLN Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1172 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 HIS A1172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115424 restraints weight = 13242.396| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.06 r_work: 0.3355 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8482 Z= 0.230 Angle : 0.655 13.754 11506 Z= 0.332 Chirality : 0.041 0.180 1380 Planarity : 0.004 0.062 1415 Dihedral : 5.978 132.340 1135 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.42 % Allowed : 25.97 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.51 (0.26), residues: 1039 helix: 1.62 (0.19), residues: 759 sheet: -0.35 (0.70), residues: 48 loop : -0.68 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.018 0.001 HIS A1156 PHE 0.040 0.002 PHE A 740 TYR 0.020 0.001 TYR A 267 ARG 0.013 0.001 ARG A1123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2391.41 seconds wall clock time: 42 minutes 57.65 seconds (2577.65 seconds total)