Starting phenix.real_space_refine on Sun May 11 22:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhx_44556/05_2025/9bhx_44556.cif" } resolution = 3.94 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= 0.000 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5316 2.51 5 N 1486 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8376 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8376 Classifications: {'peptide': 1048} Link IDs: {'PCIS': 2, 'PTRANS': 73, 'TRANS': 972} Chain breaks: 2 Time building chain proxies: 5.91, per 1000 atoms: 0.71 Number of scatterers: 8376 At special positions: 0 Unit cell: (80.704, 93.184, 161.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1541 8.00 N 1486 7.00 C 5316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.04 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 7.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 248 through 267 removed outlier: 5.347A pdb=" N TYR A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 309 removed outlier: 3.728A pdb=" N VAL A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.538A pdb=" N GLN A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N VAL A1206 " --> pdb=" O PRO A1203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.899A pdb=" N PHE A 380 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 348 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 411 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 421 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.899A pdb=" N PHE A 380 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 348 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 442 through 445 removed outlier: 6.023A pdb=" N ILE A 443 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS A 459 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 445 " --> pdb=" O HIS A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 489 removed outlier: 3.977A pdb=" N GLY A 470 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 513 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.714A pdb=" N SER A 543 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 810 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 573 through 575 removed outlier: 7.509A pdb=" N LEU A 588 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.885A pdb=" N ARG A 627 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 631 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 636 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 653 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU A 668 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER A 655 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 666 " --> pdb=" O SER A 655 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 676 through 680 removed outlier: 3.878A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 772 Processing sheet with id=AB1, first strand: chain 'A' and resid 829 through 835 removed outlier: 5.895A pdb=" N SER A 830 " --> pdb=" O LYS A 845 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 845 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 876 through 881 removed outlier: 3.886A pdb=" N ASN A 880 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 900 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 949 through 950 removed outlier: 3.533A pdb=" N HIS A 940 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG A 928 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A1183 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 930 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A1181 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 932 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 963 through 964 removed outlier: 3.678A pdb=" N TYR A 972 " --> pdb=" O HIS A 980 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 980 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 997 " --> pdb=" O LEU A 979 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.499A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1011 " --> pdb=" O ASP A1006 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP A1014 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1023 " --> pdb=" O TRP A1014 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 3.889A pdb=" N TYR A1074 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A1062 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR A1072 " --> pdb=" O ARG A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 5.534A pdb=" N ILE A1083 " --> pdb=" O LYS A1100 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A1100 " --> pdb=" O ILE A1083 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1085 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 5.534A pdb=" N ILE A1083 " --> pdb=" O LYS A1100 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A1100 " --> pdb=" O ILE A1083 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1085 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1137 through 1139 removed outlier: 3.656A pdb=" N TRP A1147 " --> pdb=" O ARG A1156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1207 through 1208 removed outlier: 3.530A pdb=" N PHE A1216 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1242 through 1248 224 hydrogen bonds defined for protein. 594 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: 3.75 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.11: 1 1.11 - 1.41: 3625 1.41 - 1.72: 4930 1.72 - 2.02: 51 2.02 - 2.33: 1 Bond restraints: 8608 Sorted by residual: bond pdb=" CG PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.503 0.806 0.697 3.40e-02 8.65e+02 4.20e+02 bond pdb=" N PRO A1111 " pdb=" CD PRO A1111 " ideal model delta sigma weight residual 1.473 1.719 -0.246 1.40e-02 5.10e+03 3.09e+02 bond pdb=" CB PRO A 460 " pdb=" CG PRO A 460 " ideal model delta sigma weight residual 1.492 2.328 -0.836 5.00e-02 4.00e+02 2.79e+02 bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.606 -0.133 1.40e-02 5.10e+03 9.01e+01 bond pdb=" C HIS A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.331 1.427 -0.096 1.27e-02 6.20e+03 5.74e+01 ... (remaining 8603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 11717 21.22 - 42.44: 3 42.44 - 63.65: 0 63.65 - 84.87: 0 84.87 - 106.09: 1 Bond angle restraints: 11721 Sorted by residual: angle pdb=" CB PRO A 460 " pdb=" CG PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 112.00 84.63 27.37 1.40e+00 5.10e-01 3.82e+02 angle pdb=" CA PRO A1111 " pdb=" N PRO A1111 " pdb=" CD PRO A1111 " ideal model delta sigma weight residual 112.00 90.00 22.00 1.40e+00 5.10e-01 2.47e+02 angle pdb=" CA PRO A 460 " pdb=" CB PRO A 460 " pdb=" CG PRO A 460 " ideal model delta sigma weight residual 104.50 85.23 19.27 1.90e+00 2.77e-01 1.03e+02 angle pdb=" N PRO A 460 " pdb=" CA PRO A 460 " pdb=" CB PRO A 460 " ideal model delta sigma weight residual 103.25 95.72 7.53 8.80e-01 1.29e+00 7.32e+01 ... (remaining 11716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4345 17.98 - 35.96: 641 35.96 - 53.95: 142 53.95 - 71.93: 20 71.93 - 89.91: 14 Dihedral angle restraints: 5162 sinusoidal: 2132 harmonic: 3030 Sorted by residual: dihedral pdb=" CB CYS A 239 " pdb=" SG CYS A 239 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual -86.00 -155.35 69.35 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CA PRO A 923 " pdb=" C PRO A 923 " pdb=" N LEU A 924 " pdb=" CA LEU A 924 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA GLN A 898 " pdb=" C GLN A 898 " pdb=" N LEU A 899 " pdb=" CA LEU A 899 " ideal model delta harmonic sigma weight residual 180.00 -158.45 -21.55 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1083 0.065 - 0.130: 153 0.130 - 0.195: 5 0.195 - 0.260: 2 0.260 - 0.325: 1 Chirality restraints: 1244 Sorted by residual: chirality pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" C PRO A 460 " pdb=" CB PRO A 460 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA GLU A 434 " pdb=" N GLU A 434 " pdb=" C GLU A 434 " pdb=" CB GLU A 434 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO A 433 " pdb=" N PRO A 433 " pdb=" C PRO A 433 " pdb=" CB PRO A 433 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1241 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1187 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO A1188 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO A1188 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A1188 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1110 " 0.102 5.00e-02 4.00e+02 1.28e-01 2.64e+01 pdb=" N PRO A1111 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO A1111 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1111 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1140 " -0.088 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO A1141 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO A1141 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A1141 " -0.067 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 21 2.31 - 2.96: 3994 2.96 - 3.60: 12027 3.60 - 4.25: 18260 4.25 - 4.90: 29730 Nonbonded interactions: 64032 Sorted by model distance: nonbonded pdb=" NH1 ARG A 550 " pdb=" O GLN A 570 " model vdw 1.661 3.120 nonbonded pdb=" NH1 ARG A 550 " pdb=" C GLN A 570 " model vdw 1.724 3.350 nonbonded pdb=" OE1 GLU A 846 " pdb=" OH TYR A 863 " model vdw 1.792 3.040 nonbonded pdb=" OD1 ASP A 657 " pdb=" N LEU A 658 " model vdw 1.941 3.120 nonbonded pdb=" O PRO A1111 " pdb=" CD PRO A1111 " model vdw 2.141 3.440 ... (remaining 64027 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: 7.810 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 24.630 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.013 0.836 8615 Z= 0.449 Angle : 1.344 106.088 11735 Z= 0.588 Chirality : 0.046 0.325 1244 Planarity : 0.009 0.139 1542 Dihedral : 17.516 89.909 3189 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.72 % Favored : 92.80 % Rotamer: Outliers : 0.44 % Allowed : 30.79 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.38 (0.25), residues: 1042 helix: 1.02 (0.67), residues: 63 sheet: -0.48 (0.28), residues: 333 loop : -1.39 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 695 HIS 0.008 0.001 HIS A 459 PHE 0.011 0.001 PHE A 735 TYR 0.070 0.002 TYR A 422 ARG 0.003 0.000 ARG A1008 Details of bonding type rmsd hydrogen bonds : bond 0.23843 ( 213) hydrogen bonds : angle 10.56516 ( 594) SS BOND : bond 0.00361 ( 7) SS BOND : angle 1.18933 ( 14) covalent geometry : bond 0.01314 ( 8608) covalent geometry : angle 1.34369 (11721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 0.1914 time to fit residues: 27.8687 Evaluate side-chains 98 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 648 GLN A 697 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154216 restraints weight = 13666.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153060 restraints weight = 18410.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154418 restraints weight = 16678.436| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8615 Z= 0.168 Angle : 0.712 12.104 11735 Z= 0.357 Chirality : 0.045 0.154 1244 Planarity : 0.006 0.070 1542 Dihedral : 4.950 23.169 1154 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.29 % Favored : 92.32 % Rotamer: Outliers : 4.32 % Allowed : 25.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.32 (0.26), residues: 1042 helix: 1.12 (0.65), residues: 64 sheet: -0.49 (0.26), residues: 359 loop : -1.35 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 695 HIS 0.006 0.001 HIS A 457 PHE 0.018 0.002 PHE A1096 TYR 0.014 0.002 TYR A 351 ARG 0.007 0.001 ARG A 550 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 213) hydrogen bonds : angle 7.25135 ( 594) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.98972 ( 14) covalent geometry : bond 0.00402 ( 8608) covalent geometry : angle 0.71154 (11721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ARG cc_start: 0.8000 (pmt-80) cc_final: 0.7778 (ppt170) REVERT: A 400 ILE cc_start: 0.7281 (tt) cc_final: 0.7044 (tt) REVERT: A 657 ASP cc_start: 0.7540 (t0) cc_final: 0.7340 (t0) REVERT: A 1089 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7388 (m-30) outliers start: 39 outliers final: 19 residues processed: 144 average time/residue: 0.2080 time to fit residues: 41.8703 Evaluate side-chains 112 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1089 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.188736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146719 restraints weight = 13937.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145201 restraints weight = 15552.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147237 restraints weight = 15350.723| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8615 Z= 0.189 Angle : 0.700 10.979 11735 Z= 0.351 Chirality : 0.045 0.135 1244 Planarity : 0.006 0.062 1542 Dihedral : 5.052 22.884 1151 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.77 % Favored : 91.94 % Rotamer: Outliers : 5.76 % Allowed : 24.03 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.36 (0.26), residues: 1042 helix: 1.15 (0.65), residues: 64 sheet: -0.55 (0.26), residues: 368 loop : -1.38 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 586 HIS 0.006 0.001 HIS A 746 PHE 0.016 0.001 PHE A1096 TYR 0.013 0.002 TYR A 297 ARG 0.004 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 213) hydrogen bonds : angle 6.69131 ( 594) SS BOND : bond 0.00290 ( 7) SS BOND : angle 0.92160 ( 14) covalent geometry : bond 0.00456 ( 8608) covalent geometry : angle 0.69922 (11721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.5102 (OUTLIER) cc_final: 0.3780 (mpp80) REVERT: A 400 ILE cc_start: 0.7599 (tt) cc_final: 0.7391 (tt) REVERT: A 555 GLN cc_start: 0.7401 (tm-30) cc_final: 0.7182 (tm-30) REVERT: A 575 ASP cc_start: 0.8629 (p0) cc_final: 0.7648 (t70) REVERT: A 688 TRP cc_start: 0.8298 (p-90) cc_final: 0.8072 (p-90) REVERT: A 1041 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8310 (t0) REVERT: A 1086 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8067 (p90) outliers start: 52 outliers final: 34 residues processed: 139 average time/residue: 0.1907 time to fit residues: 37.3621 Evaluate side-chains 128 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 0.0570 chunk 102 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.189786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148944 restraints weight = 13621.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145823 restraints weight = 15007.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.148703 restraints weight = 14945.970| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8615 Z= 0.137 Angle : 0.650 10.395 11735 Z= 0.322 Chirality : 0.043 0.142 1244 Planarity : 0.006 0.059 1542 Dihedral : 4.801 22.101 1151 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.10 % Favored : 92.61 % Rotamer: Outliers : 5.87 % Allowed : 24.70 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.26 (0.26), residues: 1042 helix: 1.43 (0.65), residues: 64 sheet: -0.40 (0.28), residues: 342 loop : -1.36 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 695 HIS 0.006 0.001 HIS A 746 PHE 0.008 0.001 PHE A1239 TYR 0.013 0.001 TYR A 351 ARG 0.006 0.000 ARG A1276 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 213) hydrogen bonds : angle 6.33487 ( 594) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.82194 ( 14) covalent geometry : bond 0.00334 ( 8608) covalent geometry : angle 0.64942 (11721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7572 (tt) cc_final: 0.7356 (tt) REVERT: A 575 ASP cc_start: 0.8547 (p0) cc_final: 0.7645 (t70) REVERT: A 576 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8672 (pt) REVERT: A 688 TRP cc_start: 0.8241 (p-90) cc_final: 0.8009 (p-90) REVERT: A 862 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 1006 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 1045 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7968 (mt) REVERT: A 1086 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7964 (p90) outliers start: 53 outliers final: 36 residues processed: 140 average time/residue: 0.1756 time to fit residues: 35.9492 Evaluate side-chains 135 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.147559 restraints weight = 13621.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.145617 restraints weight = 15389.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147632 restraints weight = 15927.855| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8615 Z= 0.147 Angle : 0.660 12.316 11735 Z= 0.325 Chirality : 0.043 0.144 1244 Planarity : 0.005 0.060 1542 Dihedral : 4.793 22.003 1151 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 7.20 % Allowed : 23.92 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.24 (0.26), residues: 1042 helix: 1.38 (0.65), residues: 64 sheet: -0.42 (0.29), residues: 332 loop : -1.31 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 695 HIS 0.004 0.001 HIS A 445 PHE 0.008 0.001 PHE A1096 TYR 0.011 0.001 TYR A 351 ARG 0.005 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 213) hydrogen bonds : angle 6.18997 ( 594) SS BOND : bond 0.00254 ( 7) SS BOND : angle 0.82119 ( 14) covalent geometry : bond 0.00361 ( 8608) covalent geometry : angle 0.66003 (11721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 96 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7960 (p0) REVERT: A 400 ILE cc_start: 0.7728 (tt) cc_final: 0.7456 (tt) REVERT: A 565 MET cc_start: 0.8252 (ttp) cc_final: 0.7870 (ttt) REVERT: A 575 ASP cc_start: 0.8629 (p0) cc_final: 0.7864 (t70) REVERT: A 576 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8784 (pt) REVERT: A 688 TRP cc_start: 0.8268 (p-90) cc_final: 0.8042 (p-90) REVERT: A 695 TRP cc_start: 0.8028 (m100) cc_final: 0.7762 (m100) REVERT: A 862 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7859 (p) REVERT: A 920 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: A 1041 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (t0) REVERT: A 1086 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7855 (p90) outliers start: 65 outliers final: 40 residues processed: 150 average time/residue: 0.1826 time to fit residues: 39.4103 Evaluate side-chains 141 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.0870 chunk 85 optimal weight: 0.4980 chunk 70 optimal weight: 0.0270 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.187233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148308 restraints weight = 13558.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146488 restraints weight = 15419.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148599 restraints weight = 14898.188| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8615 Z= 0.114 Angle : 0.641 11.511 11735 Z= 0.314 Chirality : 0.043 0.146 1244 Planarity : 0.005 0.058 1542 Dihedral : 4.614 20.688 1151 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.95 % Favored : 93.86 % Rotamer: Outliers : 5.98 % Allowed : 25.03 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.16 (0.26), residues: 1042 helix: 1.54 (0.66), residues: 64 sheet: -0.46 (0.28), residues: 338 loop : -1.21 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 586 HIS 0.004 0.001 HIS A 746 PHE 0.012 0.001 PHE A 337 TYR 0.010 0.001 TYR A 351 ARG 0.005 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 213) hydrogen bonds : angle 5.99171 ( 594) SS BOND : bond 0.00236 ( 7) SS BOND : angle 0.74918 ( 14) covalent geometry : bond 0.00286 ( 8608) covalent geometry : angle 0.64095 (11721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 100 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8150 (ttp) cc_final: 0.7774 (ttt) REVERT: A 575 ASP cc_start: 0.8559 (p0) cc_final: 0.7665 (t70) REVERT: A 688 TRP cc_start: 0.8171 (p-90) cc_final: 0.7915 (p-90) REVERT: A 727 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7322 (tt) REVERT: A 1086 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7837 (p90) outliers start: 54 outliers final: 36 residues processed: 141 average time/residue: 0.1834 time to fit residues: 37.4113 Evaluate side-chains 127 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.184528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146879 restraints weight = 13557.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144459 restraints weight = 17866.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145959 restraints weight = 16741.843| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8615 Z= 0.145 Angle : 0.667 11.087 11735 Z= 0.330 Chirality : 0.043 0.143 1244 Planarity : 0.006 0.111 1542 Dihedral : 4.757 21.531 1151 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.39 % Favored : 92.42 % Rotamer: Outliers : 5.54 % Allowed : 25.47 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.19 (0.26), residues: 1042 helix: 1.55 (0.66), residues: 64 sheet: -0.44 (0.29), residues: 331 loop : -1.25 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 695 HIS 0.016 0.001 HIS A 986 PHE 0.009 0.001 PHE A 337 TYR 0.009 0.001 TYR A1013 ARG 0.006 0.000 ARG A 920 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 213) hydrogen bonds : angle 5.94705 ( 594) SS BOND : bond 0.00234 ( 7) SS BOND : angle 0.77980 ( 14) covalent geometry : bond 0.00358 ( 8608) covalent geometry : angle 0.66734 (11721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8217 (p0) cc_final: 0.7859 (p0) REVERT: A 565 MET cc_start: 0.8166 (ttp) cc_final: 0.7803 (ttt) REVERT: A 575 ASP cc_start: 0.8679 (p0) cc_final: 0.7952 (t70) REVERT: A 653 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 1086 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7923 (p90) outliers start: 50 outliers final: 44 residues processed: 135 average time/residue: 0.1723 time to fit residues: 34.5586 Evaluate side-chains 133 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.148020 restraints weight = 13589.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145440 restraints weight = 16669.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147662 restraints weight = 15763.261| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8615 Z= 0.123 Angle : 0.682 10.786 11735 Z= 0.333 Chirality : 0.043 0.144 1244 Planarity : 0.006 0.079 1542 Dihedral : 4.671 20.801 1151 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.28 % Rotamer: Outliers : 5.65 % Allowed : 26.25 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.19 (0.26), residues: 1042 helix: 1.40 (0.67), residues: 64 sheet: -0.47 (0.29), residues: 328 loop : -1.22 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 688 HIS 0.013 0.001 HIS A 986 PHE 0.009 0.001 PHE A 337 TYR 0.009 0.001 TYR A 429 ARG 0.005 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 213) hydrogen bonds : angle 5.96214 ( 594) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.74639 ( 14) covalent geometry : bond 0.00303 ( 8608) covalent geometry : angle 0.68217 (11721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 95 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 565 MET cc_start: 0.8266 (ttp) cc_final: 0.7918 (ttt) REVERT: A 575 ASP cc_start: 0.8650 (p0) cc_final: 0.7941 (t70) REVERT: A 576 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8699 (pt) REVERT: A 653 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7777 (mm) REVERT: A 688 TRP cc_start: 0.8130 (p-90) cc_final: 0.7916 (p-90) REVERT: A 1086 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7845 (p90) REVERT: A 1199 MET cc_start: 0.6174 (ppp) cc_final: 0.5884 (ppp) outliers start: 51 outliers final: 44 residues processed: 133 average time/residue: 0.1783 time to fit residues: 34.7602 Evaluate side-chains 138 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 chunk 96 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.186610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147920 restraints weight = 13671.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145690 restraints weight = 15530.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147716 restraints weight = 15108.305| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8615 Z= 0.119 Angle : 0.687 10.573 11735 Z= 0.335 Chirality : 0.043 0.144 1244 Planarity : 0.005 0.063 1542 Dihedral : 4.601 19.764 1151 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % Rotamer: Outliers : 5.76 % Allowed : 26.02 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.16 (0.26), residues: 1042 helix: 1.33 (0.67), residues: 64 sheet: -0.34 (0.29), residues: 328 loop : -1.25 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 586 HIS 0.011 0.001 HIS A 986 PHE 0.008 0.001 PHE A 337 TYR 0.008 0.001 TYR A 863 ARG 0.005 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 213) hydrogen bonds : angle 5.92800 ( 594) SS BOND : bond 0.00217 ( 7) SS BOND : angle 0.73786 ( 14) covalent geometry : bond 0.00292 ( 8608) covalent geometry : angle 0.68703 (11721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 92 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7838 (p0) REVERT: A 430 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6769 (tm-30) REVERT: A 565 MET cc_start: 0.8246 (ttp) cc_final: 0.7914 (ttt) REVERT: A 575 ASP cc_start: 0.8669 (p0) cc_final: 0.7935 (t70) REVERT: A 576 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8655 (pt) REVERT: A 653 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7769 (mm) REVERT: A 727 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 1041 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8356 (t0) REVERT: A 1086 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7781 (p90) REVERT: A 1199 MET cc_start: 0.6173 (ppp) cc_final: 0.5816 (ppp) outliers start: 52 outliers final: 44 residues processed: 133 average time/residue: 0.1722 time to fit residues: 33.4557 Evaluate side-chains 138 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 88 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.183294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144913 restraints weight = 13476.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142212 restraints weight = 16604.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143952 restraints weight = 15932.929| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8615 Z= 0.170 Angle : 0.728 10.604 11735 Z= 0.357 Chirality : 0.044 0.144 1244 Planarity : 0.006 0.078 1542 Dihedral : 4.775 21.359 1151 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.65 % Rotamer: Outliers : 5.76 % Allowed : 26.25 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -1.24 (0.26), residues: 1042 helix: 1.23 (0.66), residues: 64 sheet: -0.55 (0.29), residues: 334 loop : -1.20 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 695 HIS 0.010 0.001 HIS A 986 PHE 0.011 0.001 PHE A1096 TYR 0.010 0.001 TYR A 863 ARG 0.003 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 213) hydrogen bonds : angle 6.01532 ( 594) SS BOND : bond 0.00229 ( 7) SS BOND : angle 0.79385 ( 14) covalent geometry : bond 0.00417 ( 8608) covalent geometry : angle 0.72749 (11721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 89 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7846 (p0) REVERT: A 565 MET cc_start: 0.8276 (ttp) cc_final: 0.7967 (ttt) REVERT: A 575 ASP cc_start: 0.8679 (p0) cc_final: 0.8075 (t70) REVERT: A 576 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8719 (pt) REVERT: A 653 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 1041 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8367 (t0) REVERT: A 1086 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8065 (p90) REVERT: A 1199 MET cc_start: 0.6157 (ppp) cc_final: 0.5756 (ppp) outliers start: 52 outliers final: 40 residues processed: 131 average time/residue: 0.1818 time to fit residues: 34.4441 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 85 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.181770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142779 restraints weight = 13748.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140850 restraints weight = 17218.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142494 restraints weight = 15331.080| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8615 Z= 0.188 Angle : 0.754 10.487 11735 Z= 0.372 Chirality : 0.045 0.171 1244 Planarity : 0.006 0.067 1542 Dihedral : 5.013 22.773 1151 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.97 % Favored : 91.84 % Rotamer: Outliers : 5.20 % Allowed : 26.69 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1042 helix: 0.93 (0.65), residues: 64 sheet: -0.56 (0.29), residues: 335 loop : -1.25 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 695 HIS 0.009 0.001 HIS A 986 PHE 0.012 0.001 PHE A 687 TYR 0.010 0.002 TYR A 863 ARG 0.005 0.000 ARG A1156 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 213) hydrogen bonds : angle 6.18056 ( 594) SS BOND : bond 0.00252 ( 7) SS BOND : angle 0.85313 ( 14) covalent geometry : bond 0.00460 ( 8608) covalent geometry : angle 0.75362 (11721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2870.76 seconds wall clock time: 51 minutes 57.72 seconds (3117.72 seconds total)