Starting phenix.real_space_refine on Wed Sep 17 11:51:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhx_44556/09_2025/9bhx_44556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhx_44556/09_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_44556/09_2025/9bhx_44556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhx_44556/09_2025/9bhx_44556.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhx_44556/09_2025/9bhx_44556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhx_44556/09_2025/9bhx_44556.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.84, per 1000 atoms: 0.22 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: 0.55 Conformation dependent library (CDL) restraints added in 250.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.32 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: 1.53 Time building geometry restraints manager: 0.75 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: 3.600 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.630 ------------------------------------------------------------------------------- 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 : 20.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (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 ARG 0.003 0.000 ARG A1008 TYR 0.070 0.002 TYR A 422 PHE 0.011 0.001 PHE A 735 TRP 0.019 0.002 TRP A 695 HIS 0.008 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.01314 ( 8608) covalent geometry : angle 1.34369 (11721) SS BOND : bond 0.00361 ( 7) SS BOND : angle 1.18933 ( 14) hydrogen bonds : bond 0.23843 ( 213) hydrogen bonds : angle 10.56516 ( 594) *********************** 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 : 0.327 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: 0.0861 time to fit residues: 12.5931 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 : 0.309 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150390 restraints weight = 13690.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149935 restraints weight = 17115.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151325 restraints weight = 16991.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152748 restraints weight = 10202.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153612 restraints weight = 8633.313| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8615 Z= 0.193 Angle : 0.732 11.997 11735 Z= 0.367 Chirality : 0.045 0.152 1244 Planarity : 0.007 0.071 1542 Dihedral : 5.049 23.669 1154 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.58 % Favored : 92.03 % Rotamer: Outliers : 4.54 % Allowed : 25.14 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.26), residues: 1042 helix: 1.08 (0.65), residues: 64 sheet: -0.57 (0.26), residues: 362 loop : -1.36 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 550 TYR 0.014 0.002 TYR A 351 PHE 0.021 0.002 PHE A1096 TRP 0.023 0.002 TRP A 695 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8608) covalent geometry : angle 0.73187 (11721) SS BOND : bond 0.00330 ( 7) SS BOND : angle 1.02616 ( 14) hydrogen bonds : bond 0.04338 ( 213) hydrogen bonds : angle 7.27256 ( 594) *********************** 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 155 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7483 (tt) cc_final: 0.7261 (tt) REVERT: A 657 ASP cc_start: 0.7623 (t0) cc_final: 0.7404 (t0) REVERT: A 696 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8084 (ptt180) REVERT: A 1086 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8070 (p90) outliers start: 41 outliers final: 23 residues processed: 147 average time/residue: 0.0923 time to fit residues: 19.0960 Evaluate side-chains 117 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 456 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 647 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 696 ARG 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 881 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 1071 VAL Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1086 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 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 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 = 0.4304 r_free = 0.4304 target = 0.188883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152773 restraints weight = 13626.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.151303 restraints weight = 18280.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152699 restraints weight = 17090.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156156 restraints weight = 11126.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.156531 restraints weight = 7804.923| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8615 Z= 0.150 Angle : 0.672 11.014 11735 Z= 0.336 Chirality : 0.044 0.137 1244 Planarity : 0.006 0.061 1542 Dihedral : 4.921 22.002 1151 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.10 % Favored : 92.61 % Rotamer: Outliers : 5.32 % Allowed : 24.92 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.26), residues: 1042 helix: 1.22 (0.65), residues: 64 sheet: -0.53 (0.26), residues: 370 loop : -1.35 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1156 TYR 0.013 0.002 TYR A 297 PHE 0.011 0.001 PHE A1096 TRP 0.035 0.002 TRP A 586 HIS 0.006 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8608) covalent geometry : angle 0.67144 (11721) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.89804 ( 14) hydrogen bonds : bond 0.03710 ( 213) hydrogen bonds : angle 6.72253 ( 594) *********************** 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 153 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 105 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7405 (tt) cc_final: 0.7188 (tt) REVERT: A 575 ASP cc_start: 0.8537 (p0) cc_final: 0.7480 (t70) REVERT: A 696 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8098 (ptt180) REVERT: A 727 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7397 (tt) REVERT: A 862 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 1006 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7606 (p0) outliers start: 48 outliers final: 30 residues processed: 143 average time/residue: 0.0896 time to fit residues: 18.2667 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 473 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 679 VAL Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 696 ARG 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 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 901 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL 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 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 5 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 2 optimal weight: 0.0470 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 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 = 0.4330 r_free = 0.4330 target = 0.192489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152194 restraints weight = 14035.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149660 restraints weight = 17642.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152416 restraints weight = 14677.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153991 restraints weight = 9557.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.154641 restraints weight = 8983.109| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2070 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= 0.121 Angle : 0.645 10.479 11735 Z= 0.318 Chirality : 0.043 0.143 1244 Planarity : 0.006 0.057 1542 Dihedral : 4.706 21.318 1151 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.01 % Favored : 92.80 % Rotamer: Outliers : 5.54 % Allowed : 25.36 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.26), residues: 1042 helix: 1.42 (0.66), residues: 64 sheet: -0.49 (0.27), residues: 353 loop : -1.31 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.011 0.001 TYR A 351 PHE 0.007 0.001 PHE A1239 TRP 0.025 0.002 TRP A 695 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8608) covalent geometry : angle 0.64486 (11721) SS BOND : bond 0.00245 ( 7) SS BOND : angle 0.77756 ( 14) hydrogen bonds : bond 0.03234 ( 213) hydrogen bonds : angle 6.35348 ( 594) *********************** 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 156 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7284 (tt) cc_final: 0.7068 (tt) REVERT: A 575 ASP cc_start: 0.8519 (p0) cc_final: 0.7481 (t70) REVERT: A 688 TRP cc_start: 0.8261 (p-90) cc_final: 0.8040 (p-90) REVERT: A 727 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7264 (tt) REVERT: A 1041 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8422 (t0) REVERT: A 1086 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7994 (p90) outliers start: 50 outliers final: 29 residues processed: 144 average time/residue: 0.0870 time to fit residues: 17.8658 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER 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 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 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 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 991 CYS 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 1157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- 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** A1092 GLN A1124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.184954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147028 restraints weight = 13868.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145944 restraints weight = 19816.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147812 restraints weight = 18930.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149375 restraints weight = 10994.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150521 restraints weight = 9340.241| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 8615 Z= 0.275 Angle : 0.767 12.421 11735 Z= 0.383 Chirality : 0.046 0.153 1244 Planarity : 0.006 0.064 1542 Dihedral : 5.353 25.121 1151 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.93 % Favored : 90.88 % Rotamer: Outliers : 8.19 % Allowed : 23.48 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.26), residues: 1042 helix: 1.23 (0.64), residues: 64 sheet: -0.67 (0.27), residues: 358 loop : -1.43 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 930 TYR 0.015 0.002 TYR A 351 PHE 0.019 0.002 PHE A1096 TRP 0.031 0.002 TRP A 695 HIS 0.008 0.002 HIS A 529 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 8608) covalent geometry : angle 0.76701 (11721) SS BOND : bond 0.00333 ( 7) SS BOND : angle 0.99012 ( 14) hydrogen bonds : bond 0.03779 ( 213) hydrogen bonds : angle 6.57077 ( 594) *********************** 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 168 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 94 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.5619 (OUTLIER) cc_final: 0.4183 (mpp80) REVERT: A 388 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 565 MET cc_start: 0.8213 (ttp) cc_final: 0.7805 (ttt) REVERT: A 575 ASP cc_start: 0.8692 (p0) cc_final: 0.8190 (t70) REVERT: A 576 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8743 (pt) REVERT: A 862 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7952 (p) REVERT: A 974 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8263 (t) REVERT: A 997 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 1041 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8364 (t0) REVERT: A 1086 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.8510 (p90) REVERT: A 1097 TRP cc_start: 0.8571 (p90) cc_final: 0.8218 (p90) REVERT: A 1224 THR cc_start: 0.7874 (t) cc_final: 0.7330 (p) outliers start: 74 outliers final: 47 residues processed: 157 average time/residue: 0.0744 time to fit residues: 17.3137 Evaluate side-chains 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 91 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG 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 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 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 504 THR 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 576 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 647 ASN 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 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 808 CYS 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 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 962 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1004 THR 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 1105 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 10 optimal weight: 0.0470 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.183675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144922 restraints weight = 13180.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142351 restraints weight = 12956.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144756 restraints weight = 13911.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146084 restraints weight = 8737.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147253 restraints weight = 7702.977| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8615 Z= 0.126 Angle : 0.670 11.389 11735 Z= 0.327 Chirality : 0.044 0.146 1244 Planarity : 0.006 0.059 1542 Dihedral : 4.873 22.986 1151 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.33 % Favored : 93.47 % Rotamer: Outliers : 5.65 % Allowed : 26.80 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.26), residues: 1042 helix: 1.37 (0.67), residues: 64 sheet: -0.49 (0.29), residues: 336 loop : -1.29 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1156 TYR 0.012 0.001 TYR A 351 PHE 0.013 0.001 PHE A 337 TRP 0.025 0.002 TRP A 688 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8608) covalent geometry : angle 0.67013 (11721) SS BOND : bond 0.00262 ( 7) SS BOND : angle 0.82717 ( 14) hydrogen bonds : bond 0.03102 ( 213) hydrogen bonds : angle 6.27121 ( 594) *********************** 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 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 101 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 PHE cc_start: 0.6972 (m-80) cc_final: 0.6709 (m-80) REVERT: A 388 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7953 (p0) REVERT: A 565 MET cc_start: 0.8335 (ttp) cc_final: 0.7983 (ttt) REVERT: A 575 ASP cc_start: 0.8578 (p0) cc_final: 0.7875 (t70) REVERT: A 576 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8723 (pt) REVERT: A 688 TRP cc_start: 0.8262 (p-90) cc_final: 0.8026 (p-90) REVERT: A 974 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8114 (t) REVERT: A 1041 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (t0) REVERT: A 1086 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7857 (p90) outliers start: 51 outliers final: 31 residues processed: 143 average time/residue: 0.0797 time to fit residues: 16.5818 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 498 SER 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 556 SER Chi-restraints excluded: chain A residue 576 ILE 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 785 ILE Chi-restraints excluded: chain A residue 787 VAL 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 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR 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 1197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.178805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131445 restraints weight = 13501.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131306 restraints weight = 10484.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131546 restraints weight = 8643.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132019 restraints weight = 9057.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132324 restraints weight = 8086.700| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8615 Z= 0.225 Angle : 0.725 11.221 11735 Z= 0.360 Chirality : 0.045 0.141 1244 Planarity : 0.006 0.063 1542 Dihedral : 5.191 24.183 1151 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.73 % Favored : 91.07 % Rotamer: Outliers : 6.09 % Allowed : 26.47 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.26), residues: 1042 helix: 1.30 (0.65), residues: 64 sheet: -0.59 (0.29), residues: 350 loop : -1.37 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1156 TYR 0.013 0.002 TYR A 405 PHE 0.014 0.002 PHE A1096 TRP 0.033 0.002 TRP A 695 HIS 0.015 0.002 HIS A 986 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8608) covalent geometry : angle 0.72437 (11721) SS BOND : bond 0.00289 ( 7) SS BOND : angle 0.94023 ( 14) hydrogen bonds : bond 0.03395 ( 213) hydrogen bonds : angle 6.29590 ( 594) *********************** 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 148 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.4191 (mpp80) REVERT: A 388 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 463 PHE cc_start: 0.7932 (m-80) cc_final: 0.7473 (m-10) REVERT: A 575 ASP cc_start: 0.8769 (p0) cc_final: 0.8254 (t70) REVERT: A 576 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8732 (pt) REVERT: A 688 TRP cc_start: 0.8450 (p-90) cc_final: 0.8247 (p-90) REVERT: A 974 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8241 (t) REVERT: A 997 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (mm) REVERT: A 1041 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8513 (t0) REVERT: A 1086 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 1097 TRP cc_start: 0.8621 (p90) cc_final: 0.8368 (p90) outliers start: 55 outliers final: 43 residues processed: 138 average time/residue: 0.0718 time to fit residues: 14.7727 Evaluate side-chains 136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 ARG 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 403 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 443 ILE 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 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE 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 576 ILE 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 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 805 LEU Chi-restraints excluded: chain A residue 808 CYS 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 955 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1004 THR 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 1197 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 0.0870 chunk 84 optimal weight: 0.3980 chunk 79 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 986 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.182396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143914 restraints weight = 13389.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142042 restraints weight = 16067.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144295 restraints weight = 16038.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145554 restraints weight = 9712.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146395 restraints weight = 8687.286| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8615 Z= 0.129 Angle : 0.669 10.686 11735 Z= 0.331 Chirality : 0.044 0.143 1244 Planarity : 0.006 0.061 1542 Dihedral : 4.889 22.513 1151 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % Rotamer: Outliers : 5.65 % Allowed : 26.58 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.26), residues: 1042 helix: 1.24 (0.66), residues: 64 sheet: -0.62 (0.29), residues: 342 loop : -1.24 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1156 TYR 0.008 0.001 TYR A1108 PHE 0.018 0.001 PHE A 337 TRP 0.026 0.002 TRP A 695 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8608) covalent geometry : angle 0.66917 (11721) SS BOND : bond 0.00261 ( 7) SS BOND : angle 0.80982 ( 14) hydrogen bonds : bond 0.02992 ( 213) hydrogen bonds : angle 6.17984 ( 594) *********************** 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 : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7835 (p0) REVERT: A 400 ILE cc_start: 0.8937 (tt) cc_final: 0.8681 (tt) REVERT: A 575 ASP cc_start: 0.8612 (p0) cc_final: 0.8013 (t70) REVERT: A 576 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8709 (pt) REVERT: A 653 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 688 TRP cc_start: 0.8263 (p-90) cc_final: 0.8038 (p-90) REVERT: A 844 TRP cc_start: 0.8240 (p90) cc_final: 0.7894 (p90) REVERT: A 974 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8194 (t) REVERT: A 1086 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7752 (p90) REVERT: A 1108 TYR cc_start: 0.6958 (m-80) cc_final: 0.6581 (m-10) outliers start: 51 outliers final: 36 residues processed: 134 average time/residue: 0.0721 time to fit residues: 14.4062 Evaluate side-chains 131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 550 ARG 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 686 ILE 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 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 935 GLN Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 986 HIS ** 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 = 0.4222 r_free = 0.4222 target = 0.181994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143641 restraints weight = 13447.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142632 restraints weight = 15842.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144377 restraints weight = 15697.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146201 restraints weight = 9365.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147455 restraints weight = 7756.841| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3343 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= 0.148 Angle : 0.683 10.635 11735 Z= 0.338 Chirality : 0.044 0.144 1244 Planarity : 0.006 0.062 1542 Dihedral : 4.878 22.026 1151 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.06 % Favored : 91.75 % Rotamer: Outliers : 5.20 % Allowed : 26.91 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.26), residues: 1042 helix: 1.19 (0.66), residues: 64 sheet: -0.58 (0.29), residues: 340 loop : -1.28 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.022 0.001 TYR A 297 PHE 0.017 0.001 PHE A 337 TRP 0.030 0.002 TRP A 586 HIS 0.010 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8608) covalent geometry : angle 0.68252 (11721) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.81486 ( 14) hydrogen bonds : bond 0.03014 ( 213) hydrogen bonds : angle 6.11521 ( 594) *********************** 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 139 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7855 (p0) REVERT: A 575 ASP cc_start: 0.8626 (p0) cc_final: 0.8052 (t70) REVERT: A 576 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8687 (pt) REVERT: A 653 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7882 (mm) REVERT: A 688 TRP cc_start: 0.8328 (p-90) cc_final: 0.8111 (p-90) REVERT: A 817 GLU cc_start: 0.6436 (tm-30) cc_final: 0.5741 (tm-30) REVERT: A 974 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 1086 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7464 (p90) outliers start: 47 outliers final: 38 residues processed: 128 average time/residue: 0.0730 time to fit residues: 13.9975 Evaluate side-chains 132 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 539 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 550 ARG 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 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 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 89 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** A 986 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143534 restraints weight = 13579.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140479 restraints weight = 14528.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142521 restraints weight = 15236.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143878 restraints weight = 9816.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144459 restraints weight = 8798.379| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3416 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= 0.140 Angle : 0.684 10.771 11735 Z= 0.337 Chirality : 0.043 0.141 1244 Planarity : 0.006 0.063 1542 Dihedral : 4.812 21.526 1151 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.81 % Favored : 92.99 % Rotamer: Outliers : 5.54 % Allowed : 27.13 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.26), residues: 1042 helix: 1.10 (0.65), residues: 64 sheet: -0.54 (0.29), residues: 335 loop : -1.30 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1156 TYR 0.009 0.001 TYR A 863 PHE 0.017 0.001 PHE A 337 TRP 0.026 0.002 TRP A 695 HIS 0.010 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8608) covalent geometry : angle 0.68384 (11721) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.79903 ( 14) hydrogen bonds : bond 0.02989 ( 213) hydrogen bonds : angle 6.06762 ( 594) ********************** 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 136 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7880 (p0) REVERT: A 575 ASP cc_start: 0.8678 (p0) cc_final: 0.8092 (t70) REVERT: A 576 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8696 (pt) REVERT: A 653 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 688 TRP cc_start: 0.8259 (p-90) cc_final: 0.8018 (p-90) REVERT: A 974 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8240 (t) REVERT: A 1086 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7354 (p90) outliers start: 50 outliers final: 40 residues processed: 124 average time/residue: 0.0733 time to fit residues: 13.7612 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 : 0.366 ------------------------------------------------------------------------------- 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 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 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 550 ARG 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 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 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.181324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142886 restraints weight = 13536.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142577 restraints weight = 15890.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144481 restraints weight = 15114.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145508 restraints weight = 9530.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146502 restraints weight = 8466.128| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8615 Z= 0.163 Angle : 0.699 10.505 11735 Z= 0.344 Chirality : 0.044 0.201 1244 Planarity : 0.006 0.063 1542 Dihedral : 4.857 21.841 1151 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.94 % Rotamer: Outliers : 5.76 % Allowed : 26.91 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.26), residues: 1042 helix: 1.07 (0.65), residues: 64 sheet: -0.54 (0.29), residues: 335 loop : -1.30 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1156 TYR 0.037 0.002 TYR A 297 PHE 0.015 0.001 PHE A 337 TRP 0.024 0.002 TRP A 695 HIS 0.010 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8608) covalent geometry : angle 0.69868 (11721) SS BOND : bond 0.00242 ( 7) SS BOND : angle 0.81342 ( 14) hydrogen bonds : bond 0.03052 ( 213) hydrogen bonds : angle 6.07424 ( 594) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1485.42 seconds wall clock time: 26 minutes 26.13 seconds (1586.13 seconds total)