Starting phenix.real_space_refine on Thu Mar 13 01:44:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhx_44556/03_2025/9bhx_44556.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhx_44556/03_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_44556/03_2025/9bhx_44556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhx_44556/03_2025/9bhx_44556.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhx_44556/03_2025/9bhx_44556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhx_44556/03_2025/9bhx_44556.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 5316 2.51 5 N 1486 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8376 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8376 Classifications: {'peptide': 1048} Link IDs: {'PCIS': 2, 'PTRANS': 73, 'TRANS': 972} Chain breaks: 2 Time building chain proxies: 5.58, per 1000 atoms: 0.67 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: 1.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 20 sheets defined 7.7% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 248 through 267 removed outlier: 5.347A pdb=" N TYR A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 309 removed outlier: 3.728A pdb=" N VAL A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.538A pdb=" N GLN A 819 " --> pdb=" O PRO A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N VAL A1206 " --> pdb=" O PRO A1203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.899A pdb=" N PHE A 380 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 348 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 411 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU A 421 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.899A pdb=" N PHE A 380 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A 348 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 442 through 445 removed outlier: 6.023A pdb=" N ILE A 443 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N HIS A 459 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 445 " --> pdb=" O HIS A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 489 removed outlier: 3.977A pdb=" N GLY A 470 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 513 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.714A pdb=" N SER A 543 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 810 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 573 through 575 removed outlier: 7.509A pdb=" N LEU A 588 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.885A pdb=" N ARG A 627 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 631 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 636 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 653 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU A 668 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER A 655 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 666 " --> pdb=" O SER A 655 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 676 through 680 removed outlier: 3.878A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 772 Processing sheet with id=AB1, first strand: chain 'A' and resid 829 through 835 removed outlier: 5.895A pdb=" N SER A 830 " --> pdb=" O LYS A 845 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 845 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 876 through 881 removed outlier: 3.886A pdb=" N ASN A 880 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 900 " --> pdb=" O GLU A 866 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 949 through 950 removed outlier: 3.533A pdb=" N HIS A 940 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG A 928 " --> pdb=" O LEU A1183 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LEU A1183 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG A 930 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A1181 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 932 " --> pdb=" O SER A1179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 963 through 964 removed outlier: 3.678A pdb=" N TYR A 972 " --> pdb=" O HIS A 980 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS A 980 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 997 " --> pdb=" O LEU A 979 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.499A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1011 " --> pdb=" O ASP A1006 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TRP A1014 " --> pdb=" O VAL A1023 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A1023 " --> pdb=" O TRP A1014 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 3.889A pdb=" N TYR A1074 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A1062 " --> pdb=" O THR A1072 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N THR A1072 " --> pdb=" O ARG A1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 5.534A pdb=" N ILE A1083 " --> pdb=" O LYS A1100 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A1100 " --> pdb=" O ILE A1083 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1085 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 5.534A pdb=" N ILE A1083 " --> pdb=" O LYS A1100 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS A1100 " --> pdb=" O ILE A1083 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A1085 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1137 through 1139 removed outlier: 3.656A pdb=" N TRP A1147 " --> pdb=" O ARG A1156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1207 through 1208 removed outlier: 3.530A pdb=" N PHE A1216 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1242 through 1248 224 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.35 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: 21.330 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.380 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.980 ------------------------------------------------------------------------------- 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 8608 Z= 0.995 Angle : 1.344 106.088 11721 Z= 0.588 Chirality : 0.046 0.325 1244 Planarity : 0.009 0.139 1542 Dihedral : 17.516 89.909 3189 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.72 % Favored : 92.80 % Rotamer: Outliers : 0.44 % Allowed : 30.79 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1042 helix: 1.02 (0.67), residues: 63 sheet: -0.48 (0.28), residues: 333 loop : -1.39 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 695 HIS 0.008 0.001 HIS A 459 PHE 0.011 0.001 PHE A 735 TYR 0.070 0.002 TYR A 422 ARG 0.003 0.000 ARG A1008 *********************** 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 : 0.975 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: 0.2020 time to fit residues: 29.6616 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 : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 889 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 ASN A 648 GLN A 697 GLN ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.190312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154216 restraints weight = 13666.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153061 restraints weight = 18410.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.154418 restraints weight = 16678.464| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8608 Z= 0.266 Angle : 0.712 12.104 11721 Z= 0.357 Chirality : 0.045 0.154 1244 Planarity : 0.006 0.070 1542 Dihedral : 4.950 23.169 1154 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.29 % Favored : 92.32 % Rotamer: Outliers : 4.32 % Allowed : 25.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.26), residues: 1042 helix: 1.12 (0.65), residues: 64 sheet: -0.49 (0.26), residues: 359 loop : -1.35 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 695 HIS 0.006 0.001 HIS A 457 PHE 0.018 0.002 PHE A1096 TYR 0.014 0.002 TYR A 351 ARG 0.007 0.001 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ARG cc_start: 0.8000 (pmt-80) cc_final: 0.7778 (ppt170) REVERT: A 400 ILE cc_start: 0.7281 (tt) cc_final: 0.7044 (tt) REVERT: A 657 ASP cc_start: 0.7540 (t0) cc_final: 0.7340 (t0) REVERT: A 1089 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7388 (m-30) outliers start: 39 outliers final: 19 residues processed: 144 average time/residue: 0.2081 time to fit residues: 41.6615 Evaluate side-chains 112 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1089 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A1124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.186078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144938 restraints weight = 13812.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142334 restraints weight = 17868.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.144227 restraints weight = 16843.528| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8608 Z= 0.374 Angle : 0.740 11.157 11721 Z= 0.372 Chirality : 0.046 0.143 1244 Planarity : 0.006 0.067 1542 Dihedral : 5.192 23.414 1151 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.06 % Favored : 91.65 % Rotamer: Outliers : 6.20 % Allowed : 23.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.26), residues: 1042 helix: 1.15 (0.65), residues: 64 sheet: -0.63 (0.26), residues: 365 loop : -1.41 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 586 HIS 0.006 0.001 HIS A 529 PHE 0.019 0.002 PHE A1096 TYR 0.014 0.002 TYR A 405 ARG 0.006 0.001 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 96 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.5319 (OUTLIER) cc_final: 0.4024 (mpp80) REVERT: A 400 ILE cc_start: 0.7809 (tt) cc_final: 0.7602 (tt) REVERT: A 575 ASP cc_start: 0.8665 (p0) cc_final: 0.7802 (t70) REVERT: A 688 TRP cc_start: 0.8301 (p-90) cc_final: 0.8095 (p-90) REVERT: A 862 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8011 (p) REVERT: A 1041 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8360 (t0) REVERT: A 1086 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8113 (p90) outliers start: 56 outliers final: 37 residues processed: 142 average time/residue: 0.1882 time to fit residues: 38.6295 Evaluate side-chains 133 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 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 704 ILE 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 964 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.186304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149659 restraints weight = 13603.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151944 restraints weight = 19042.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152455 restraints weight = 16237.995| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8608 Z= 0.267 Angle : 0.669 10.434 11721 Z= 0.334 Chirality : 0.044 0.145 1244 Planarity : 0.006 0.063 1542 Dihedral : 4.991 23.475 1151 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.03 % Rotamer: Outliers : 5.87 % Allowed : 24.58 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1042 helix: 1.34 (0.65), residues: 64 sheet: -0.57 (0.27), residues: 366 loop : -1.35 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 695 HIS 0.006 0.001 HIS A 746 PHE 0.008 0.001 PHE A 876 TYR 0.012 0.001 TYR A 351 ARG 0.006 0.000 ARG A1156 *********************** 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 151 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.5320 (OUTLIER) cc_final: 0.3997 (mpp80) REVERT: A 400 ILE cc_start: 0.7813 (tt) cc_final: 0.7590 (tt) REVERT: A 575 ASP cc_start: 0.8651 (p0) cc_final: 0.7883 (t70) REVERT: A 576 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8713 (pt) REVERT: A 688 TRP cc_start: 0.8370 (p-90) cc_final: 0.8150 (p-90) REVERT: A 974 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8202 (t) REVERT: A 1086 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7961 (p90) REVERT: A 1089 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: A 1189 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8146 (mm) outliers start: 53 outliers final: 34 residues processed: 142 average time/residue: 0.2154 time to fit residues: 44.3772 Evaluate side-chains 130 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 90 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 686 ILE 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 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 ASP Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** A1092 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.187771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148320 restraints weight = 13540.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.147340 restraints weight = 16666.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149537 restraints weight = 15495.955| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8608 Z= 0.244 Angle : 0.675 12.395 11721 Z= 0.333 Chirality : 0.044 0.146 1244 Planarity : 0.006 0.062 1542 Dihedral : 4.927 22.837 1151 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.87 % Favored : 91.94 % Rotamer: Outliers : 7.20 % Allowed : 24.14 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1042 helix: 1.33 (0.65), residues: 64 sheet: -0.53 (0.29), residues: 339 loop : -1.28 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 695 HIS 0.004 0.001 HIS A 746 PHE 0.008 0.001 PHE A 744 TYR 0.011 0.001 TYR A 351 ARG 0.005 0.000 ARG A 920 *********************** 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 162 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 97 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7887 (p0) REVERT: A 400 ILE cc_start: 0.7854 (tt) cc_final: 0.7593 (tt) REVERT: A 575 ASP cc_start: 0.8643 (p0) cc_final: 0.7918 (t70) REVERT: A 576 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8731 (pt) REVERT: A 688 TRP cc_start: 0.8327 (p-90) cc_final: 0.8081 (p-90) REVERT: A 920 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7027 (ttp80) REVERT: A 1041 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 1086 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7819 (p90) outliers start: 65 outliers final: 44 residues processed: 152 average time/residue: 0.1763 time to fit residues: 40.5973 Evaluate side-chains 145 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 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 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 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 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 85 optimal weight: 0.0270 chunk 70 optimal weight: 0.0070 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148628 restraints weight = 13622.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.145815 restraints weight = 14636.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147618 restraints weight = 14087.668| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8608 Z= 0.186 Angle : 0.655 11.635 11721 Z= 0.320 Chirality : 0.043 0.143 1244 Planarity : 0.006 0.063 1542 Dihedral : 4.690 21.229 1151 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.14 % Favored : 93.67 % Rotamer: Outliers : 5.32 % Allowed : 25.80 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1042 helix: 1.47 (0.66), residues: 64 sheet: -0.50 (0.29), residues: 331 loop : -1.25 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 586 HIS 0.006 0.001 HIS A 746 PHE 0.020 0.001 PHE A 337 TYR 0.011 0.001 TYR A 971 ARG 0.005 0.000 ARG A 920 *********************** 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 146 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7885 (p0) REVERT: A 575 ASP cc_start: 0.8594 (p0) cc_final: 0.7712 (t70) REVERT: A 688 TRP cc_start: 0.8198 (p-90) cc_final: 0.7939 (p-90) REVERT: A 695 TRP cc_start: 0.7984 (m100) cc_final: 0.7708 (m100) REVERT: A 727 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7236 (tt) REVERT: A 844 TRP cc_start: 0.8113 (p90) cc_final: 0.7736 (p90) REVERT: A 920 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.7000 (tmm160) REVERT: A 974 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8105 (t) REVERT: A 1086 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7735 (p90) REVERT: A 1247 ASP cc_start: 0.7730 (m-30) cc_final: 0.7510 (m-30) outliers start: 48 outliers final: 33 residues processed: 135 average time/residue: 0.1853 time to fit residues: 35.9701 Evaluate side-chains 129 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 91 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 464 THR Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 920 ARG 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 1017 LEU Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 36 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 23 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.182263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.145411 restraints weight = 13582.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144559 restraints weight = 17142.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146266 restraints weight = 17376.670| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8608 Z= 0.287 Angle : 0.689 11.191 11721 Z= 0.340 Chirality : 0.044 0.146 1244 Planarity : 0.006 0.063 1542 Dihedral : 4.900 22.374 1151 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.46 % Rotamer: Outliers : 6.31 % Allowed : 24.81 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1042 helix: 1.56 (0.66), residues: 64 sheet: -0.50 (0.29), residues: 340 loop : -1.29 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 989 HIS 0.016 0.002 HIS A 986 PHE 0.015 0.001 PHE A 337 TYR 0.010 0.002 TYR A1108 ARG 0.005 0.000 ARG A 920 *********************** 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: 57 poor density : 91 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 565 MET cc_start: 0.8241 (ttp) cc_final: 0.7858 (ttt) REVERT: A 575 ASP cc_start: 0.8651 (p0) cc_final: 0.8070 (t70) REVERT: A 576 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8693 (pt) REVERT: A 688 TRP cc_start: 0.8311 (p-90) cc_final: 0.8079 (p-90) REVERT: A 920 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.7012 (ttp80) REVERT: A 974 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 1041 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8442 (t0) REVERT: A 1086 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7770 (p90) outliers start: 57 outliers final: 48 residues processed: 139 average time/residue: 0.1649 time to fit residues: 34.1357 Evaluate side-chains 142 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 88 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LEU 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 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 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 686 ILE Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1105 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1197 ILE Chi-restraints excluded: chain A residue 1248 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 ** 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 = 0.4243 r_free = 0.4243 target = 0.183994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146651 restraints weight = 13662.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148848 restraints weight = 17667.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.149645 restraints weight = 15321.191| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8608 Z= 0.212 Angle : 0.676 12.431 11721 Z= 0.328 Chirality : 0.043 0.146 1244 Planarity : 0.006 0.065 1542 Dihedral : 4.753 21.824 1151 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % Rotamer: Outliers : 6.09 % Allowed : 25.80 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.26), residues: 1042 helix: 1.61 (0.66), residues: 64 sheet: -0.46 (0.29), residues: 331 loop : -1.26 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 695 HIS 0.009 0.001 HIS A 746 PHE 0.013 0.001 PHE A 337 TYR 0.008 0.001 TYR A1108 ARG 0.005 0.000 ARG A 920 *********************** 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 147 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 92 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7733 (p0) REVERT: A 565 MET cc_start: 0.8275 (ttp) cc_final: 0.7882 (ttt) REVERT: A 575 ASP cc_start: 0.8667 (p0) cc_final: 0.8020 (t70) REVERT: A 576 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8686 (pt) REVERT: A 688 TRP cc_start: 0.8265 (p-90) cc_final: 0.8016 (p-90) REVERT: A 695 TRP cc_start: 0.7932 (m100) cc_final: 0.7645 (m100) REVERT: A 920 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6975 (ttp80) REVERT: A 1041 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8447 (t0) REVERT: A 1086 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7707 (p90) outliers start: 55 outliers final: 43 residues processed: 137 average time/residue: 0.1758 time to fit residues: 34.9291 Evaluate side-chains 137 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 89 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 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 686 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 785 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 878 ILE 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 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4240 r_free = 0.4240 target = 0.183882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.144515 restraints weight = 13874.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142293 restraints weight = 15935.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144902 restraints weight = 15390.998| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8608 Z= 0.234 Angle : 0.681 11.527 11721 Z= 0.332 Chirality : 0.043 0.146 1244 Planarity : 0.006 0.066 1542 Dihedral : 4.741 21.621 1151 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.68 % Favored : 92.13 % Rotamer: Outliers : 5.65 % Allowed : 26.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.26), residues: 1042 helix: 1.57 (0.66), residues: 64 sheet: -0.49 (0.29), residues: 331 loop : -1.27 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 695 HIS 0.008 0.001 HIS A 746 PHE 0.013 0.001 PHE A 337 TYR 0.008 0.001 TYR A1108 ARG 0.005 0.000 ARG A 920 *********************** 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: 51 poor density : 88 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7826 (p0) REVERT: A 535 LYS cc_start: 0.4517 (mmtt) cc_final: 0.4306 (mmtt) REVERT: A 565 MET cc_start: 0.8392 (ttp) cc_final: 0.8052 (ttt) REVERT: A 575 ASP cc_start: 0.8659 (p0) cc_final: 0.8075 (t70) REVERT: A 576 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8671 (pt) REVERT: A 653 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7940 (mm) REVERT: A 688 TRP cc_start: 0.8263 (p-90) cc_final: 0.7999 (p-90) REVERT: A 920 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: A 1041 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (t0) REVERT: A 1086 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7844 (p90) outliers start: 51 outliers final: 43 residues processed: 130 average time/residue: 0.2074 time to fit residues: 39.4804 Evaluate side-chains 134 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 85 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 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 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 803 LYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 866 GLU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 991 CYS Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1041 ASN Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.4251 r_free = 0.4251 target = 0.183416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142883 restraints weight = 13591.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141708 restraints weight = 17097.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143278 restraints weight = 18369.189| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 8608 Z= 0.467 Angle : 0.813 11.194 11721 Z= 0.406 Chirality : 0.047 0.166 1244 Planarity : 0.006 0.066 1542 Dihedral : 5.421 25.999 1151 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.79 % Favored : 90.02 % Rotamer: Outliers : 5.54 % Allowed : 26.36 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 1042 helix: 1.15 (0.65), residues: 64 sheet: -0.73 (0.29), residues: 351 loop : -1.45 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 695 HIS 0.015 0.002 HIS A 299 PHE 0.020 0.002 PHE A1096 TYR 0.014 0.002 TYR A1005 ARG 0.009 0.001 ARG A1019 ********************** 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 140 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.4648 (mpp80) REVERT: A 388 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7779 (p0) REVERT: A 535 LYS cc_start: 0.4651 (mmtt) cc_final: 0.4372 (mmtt) REVERT: A 575 ASP cc_start: 0.8754 (p0) cc_final: 0.8373 (t0) REVERT: A 576 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8739 (pt) REVERT: A 688 TRP cc_start: 0.8390 (p-90) cc_final: 0.8146 (p-90) REVERT: A 920 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7109 (ttp80) REVERT: A 964 MET cc_start: 0.9082 (mmm) cc_final: 0.8647 (mmt) REVERT: A 1086 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7935 (p90) REVERT: A 1247 ASP cc_start: 0.7979 (m-30) cc_final: 0.7666 (m-30) outliers start: 50 outliers final: 38 residues processed: 131 average time/residue: 0.1827 time to fit residues: 34.1666 Evaluate side-chains 131 residues out of total 903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 464 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 544 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 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 882 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 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 1136 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1197 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.178118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139540 restraints weight = 13430.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137643 restraints weight = 15325.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139091 restraints weight = 17202.993| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8608 Z= 0.340 Angle : 0.742 11.040 11721 Z= 0.368 Chirality : 0.046 0.149 1244 Planarity : 0.006 0.064 1542 Dihedral : 5.217 25.333 1151 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.64 % Favored : 91.17 % Rotamer: Outliers : 5.09 % Allowed : 26.69 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 1042 helix: 1.12 (0.65), residues: 64 sheet: -0.73 (0.29), residues: 339 loop : -1.42 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 695 HIS 0.008 0.001 HIS A 746 PHE 0.011 0.002 PHE A 876 TYR 0.009 0.002 TYR A 282 ARG 0.007 0.000 ARG A1150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.26 seconds wall clock time: 50 minutes 39.40 seconds (3039.40 seconds total)