Starting phenix.real_space_refine on Wed Mar 12 20:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq4_38565/03_2025/8xq4_38565.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 46 5.16 5 C 5375 2.51 5 N 1365 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8237 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8237 Classifications: {'peptide': 1044} Link IDs: {'PTRANS': 32, 'TRANS': 1011} Chain breaks: 5 Time building chain proxies: 5.16, per 1000 atoms: 0.63 Number of scatterers: 8237 At special positions: 0 Unit cell: (83.16, 112.32, 123.12, 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 46 16.00 O 1451 8.00 N 1365 7.00 C 5375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 75.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 75 through 95 removed outlier: 4.277A pdb=" N VAL A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.914A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.678A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.505A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.807A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 253 removed outlier: 3.749A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.837A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.895A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 removed outlier: 3.703A pdb=" N ALA A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 412 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.659A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.383A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.682A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 639 through 652 removed outlier: 4.186A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 679 through 705 removed outlier: 4.278A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 727 through 753 Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 761 through 784 Processing helix chain 'A' and resid 798 through 853 removed outlier: 3.856A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 853 through 858 removed outlier: 4.019A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.663A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.960A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1069 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1122 Processing sheet with id=AA1, first strand: chain 'A' and resid 979 through 982 removed outlier: 6.230A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.534A pdb=" N VAL A1057 " --> pdb=" O ILE A 988 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.553A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 3.924A pdb=" N ASN A1154 " --> pdb=" O GLU A1159 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A1159 " --> pdb=" O ASN A1154 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1833 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2593 1.34 - 1.46: 1560 1.46 - 1.58: 4159 1.58 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8395 Sorted by residual: bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.06e+00 bond pdb=" CA ILE A 818 " pdb=" C ILE A 818 " ideal model delta sigma weight residual 1.523 1.539 -0.016 9.20e-03 1.18e+04 3.03e+00 bond pdb=" C ILE A 488 " pdb=" N PRO A 489 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.84e+00 bond pdb=" C THR A1100 " pdb=" N PRO A1101 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.23e-02 6.61e+03 2.72e+00 bond pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 1.460 1.484 -0.025 1.54e-02 4.22e+03 2.56e+00 ... (remaining 8390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11192 2.33 - 4.67: 151 4.67 - 7.00: 27 7.00 - 9.33: 11 9.33 - 11.67: 3 Bond angle restraints: 11384 Sorted by residual: angle pdb=" C VAL A 741 " pdb=" N ILE A 742 " pdb=" CA ILE A 742 " ideal model delta sigma weight residual 121.97 129.80 -7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" N ALA A 679 " pdb=" CA ALA A 679 " pdb=" C ALA A 679 " ideal model delta sigma weight residual 114.56 109.24 5.32 1.27e+00 6.20e-01 1.75e+01 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 122.46 128.30 -5.84 1.41e+00 5.03e-01 1.72e+01 angle pdb=" C HIS A 677 " pdb=" N MET A 678 " pdb=" CA MET A 678 " ideal model delta sigma weight residual 121.54 129.02 -7.48 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ILE A 413 " pdb=" CA ILE A 413 " pdb=" C ILE A 413 " ideal model delta sigma weight residual 108.82 104.33 4.49 1.22e+00 6.72e-01 1.35e+01 ... (remaining 11379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 4576 16.10 - 32.19: 349 32.19 - 48.29: 75 48.29 - 64.39: 21 64.39 - 80.48: 4 Dihedral angle restraints: 5025 sinusoidal: 1990 harmonic: 3035 Sorted by residual: dihedral pdb=" CA TYR A1083 " pdb=" C TYR A1083 " pdb=" N PRO A1084 " pdb=" CA PRO A1084 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA VAL A 252 " pdb=" C VAL A 252 " pdb=" N PHE A 253 " pdb=" CA PHE A 253 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA LEU A 754 " pdb=" C LEU A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta harmonic sigma weight residual 180.00 157.18 22.82 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1234 0.074 - 0.149: 123 0.149 - 0.223: 9 0.223 - 0.297: 1 0.297 - 0.371: 1 Chirality restraints: 1368 Sorted by residual: chirality pdb=" CB ILE A 742 " pdb=" CA ILE A 742 " pdb=" CG1 ILE A 742 " pdb=" CG2 ILE A 742 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL A 558 " pdb=" CA VAL A 558 " pdb=" CG1 VAL A 558 " pdb=" CG2 VAL A 558 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA THR A1100 " pdb=" N THR A1100 " pdb=" C THR A1100 " pdb=" CB THR A1100 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1365 not shown) Planarity restraints: 1404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 766 " 0.021 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE A 766 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 766 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 766 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 766 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 766 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 766 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LEU A 467 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 467 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 468 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 276 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.027 5.00e-02 4.00e+02 ... (remaining 1401 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1903 2.79 - 3.32: 7688 3.32 - 3.85: 13772 3.85 - 4.37: 14686 4.37 - 4.90: 27042 Nonbonded interactions: 65091 Sorted by model distance: nonbonded pdb=" O ILE A 469 " pdb=" OG1 THR A 473 " model vdw 2.267 3.040 nonbonded pdb=" O ALA A 307 " pdb=" OG1 THR A 311 " model vdw 2.305 3.040 nonbonded pdb=" O SER A 404 " pdb=" OG SER A 407 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 407 " pdb=" OG SER A 411 " model vdw 2.360 3.040 nonbonded pdb=" O THR A1081 " pdb=" OG1 THR A1081 " model vdw 2.374 3.040 ... (remaining 65086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.003 0.060 8395 Z= 0.206 Angle : 0.737 11.669 11384 Z= 0.406 Chirality : 0.046 0.371 1368 Planarity : 0.006 0.049 1404 Dihedral : 12.524 80.482 3057 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.90 % Allowed : 9.69 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1032 helix: -0.58 (0.16), residues: 765 sheet: -0.23 (0.76), residues: 46 loop : -1.82 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.002 0.000 HIS A 350 PHE 0.043 0.001 PHE A 766 TYR 0.010 0.001 TYR A 191 ARG 0.001 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8064 (p) cc_final: 0.7749 (m) REVERT: A 112 ILE cc_start: 0.8296 (mm) cc_final: 0.8062 (mm) REVERT: A 135 PRO cc_start: 0.7864 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: A 149 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 154 MET cc_start: 0.8483 (tpp) cc_final: 0.7751 (tpp) REVERT: A 155 ASP cc_start: 0.8030 (t0) cc_final: 0.7797 (t0) REVERT: A 158 THR cc_start: 0.8785 (p) cc_final: 0.8237 (p) REVERT: A 163 PHE cc_start: 0.7856 (t80) cc_final: 0.7565 (t80) REVERT: A 174 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (tp) REVERT: A 195 PHE cc_start: 0.7683 (t80) cc_final: 0.7394 (t80) REVERT: A 197 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 231 GLU cc_start: 0.7618 (tt0) cc_final: 0.7280 (tt0) REVERT: A 233 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7788 (tm-30) REVERT: A 237 ASN cc_start: 0.8043 (t0) cc_final: 0.7835 (t0) REVERT: A 246 ASN cc_start: 0.8281 (m-40) cc_final: 0.7997 (m110) REVERT: A 249 MET cc_start: 0.8270 (tmm) cc_final: 0.7968 (ttp) REVERT: A 284 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8355 (mmmm) REVERT: A 338 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8348 (mtmm) REVERT: A 354 GLU cc_start: 0.8030 (tt0) cc_final: 0.7828 (tt0) REVERT: A 363 LEU cc_start: 0.8460 (mt) cc_final: 0.7909 (mm) REVERT: A 366 MET cc_start: 0.8353 (mmm) cc_final: 0.8089 (mmm) REVERT: A 373 THR cc_start: 0.8538 (t) cc_final: 0.8326 (t) REVERT: A 375 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7957 (ttmm) REVERT: A 386 PHE cc_start: 0.8088 (t80) cc_final: 0.7529 (t80) REVERT: A 491 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8261 (ttm-80) REVERT: A 513 LYS cc_start: 0.8851 (mttt) cc_final: 0.8494 (mttm) REVERT: A 531 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: A 588 LYS cc_start: 0.8316 (tppt) cc_final: 0.7896 (tppt) REVERT: A 591 LYS cc_start: 0.8419 (mttt) cc_final: 0.7696 (mttt) REVERT: A 609 ARG cc_start: 0.8038 (mmm-85) cc_final: 0.7697 (mmm-85) REVERT: A 616 GLU cc_start: 0.7355 (pt0) cc_final: 0.7092 (pt0) REVERT: A 621 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: A 633 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8483 (mmtt) REVERT: A 671 MET cc_start: 0.5881 (mmt) cc_final: 0.5272 (mmt) REVERT: A 678 MET cc_start: 0.6303 (ppp) cc_final: 0.6045 (ppp) REVERT: A 694 PRO cc_start: 0.7797 (Cg_exo) cc_final: 0.7482 (Cg_endo) REVERT: A 697 MET cc_start: 0.7028 (mmm) cc_final: 0.6519 (mmm) REVERT: A 800 LYS cc_start: 0.6928 (ttpp) cc_final: 0.6563 (tttp) REVERT: A 824 VAL cc_start: 0.8640 (t) cc_final: 0.8415 (t) REVERT: A 825 VAL cc_start: 0.8790 (t) cc_final: 0.8464 (p) REVERT: A 832 GLN cc_start: 0.8384 (tp40) cc_final: 0.8131 (tt0) REVERT: A 837 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 910 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7803 (ttm170) REVERT: A 923 ASP cc_start: 0.7873 (p0) cc_final: 0.7601 (p0) REVERT: A 926 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 935 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7967 (mt-10) REVERT: A 981 HIS cc_start: 0.7990 (m90) cc_final: 0.7641 (m-70) REVERT: A 993 ASP cc_start: 0.7338 (p0) cc_final: 0.7137 (p0) REVERT: A 994 GLU cc_start: 0.8318 (pm20) cc_final: 0.7847 (pm20) REVERT: A 1007 LYS cc_start: 0.8456 (tttp) cc_final: 0.8251 (ttmm) REVERT: A 1044 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7437 (mt-10) REVERT: A 1045 MET cc_start: 0.8206 (ttp) cc_final: 0.7950 (ttm) REVERT: A 1066 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: A 1075 ILE cc_start: 0.8269 (mm) cc_final: 0.8044 (mm) REVERT: A 1087 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 1098 ILE cc_start: 0.8662 (tt) cc_final: 0.8458 (tt) REVERT: A 1100 THR cc_start: 0.8629 (t) cc_final: 0.8215 (p) REVERT: A 1110 GLN cc_start: 0.7386 (mp10) cc_final: 0.6888 (mp10) REVERT: A 1122 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7364 (mm-30) REVERT: A 1161 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7105 (pt) REVERT: A 1190 ARG cc_start: 0.7388 (mpt180) cc_final: 0.6959 (mmt180) outliers start: 35 outliers final: 9 residues processed: 325 average time/residue: 0.2969 time to fit residues: 127.3666 Evaluate side-chains 282 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 267 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A1114 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.136680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118059 restraints weight = 12600.317| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.05 r_work: 0.3368 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8395 Z= 0.218 Angle : 0.577 14.311 11384 Z= 0.298 Chirality : 0.040 0.183 1368 Planarity : 0.004 0.039 1404 Dihedral : 7.011 59.688 1144 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.12 % Allowed : 15.37 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1032 helix: 0.86 (0.19), residues: 763 sheet: -0.30 (0.72), residues: 48 loop : -1.46 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1112 HIS 0.003 0.001 HIS A 908 PHE 0.030 0.001 PHE A 766 TYR 0.009 0.001 TYR A 309 ARG 0.009 0.001 ARG A 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8302 (p) cc_final: 0.7992 (m) REVERT: A 112 ILE cc_start: 0.8509 (mm) cc_final: 0.8274 (mm) REVERT: A 149 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 154 MET cc_start: 0.8512 (tpp) cc_final: 0.6891 (tpp) REVERT: A 155 ASP cc_start: 0.7993 (t0) cc_final: 0.7753 (t0) REVERT: A 176 VAL cc_start: 0.8560 (p) cc_final: 0.8267 (t) REVERT: A 190 ASN cc_start: 0.8219 (p0) cc_final: 0.7979 (p0) REVERT: A 197 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 231 GLU cc_start: 0.7444 (tt0) cc_final: 0.6923 (tt0) REVERT: A 233 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7650 (tm-30) REVERT: A 246 ASN cc_start: 0.8180 (m-40) cc_final: 0.7881 (m110) REVERT: A 338 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8293 (mtmm) REVERT: A 363 LEU cc_start: 0.8449 (mt) cc_final: 0.8233 (mt) REVERT: A 375 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8086 (ttmm) REVERT: A 377 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 386 PHE cc_start: 0.8110 (t80) cc_final: 0.7518 (t80) REVERT: A 480 ILE cc_start: 0.7969 (mt) cc_final: 0.7687 (mt) REVERT: A 486 ILE cc_start: 0.8478 (mp) cc_final: 0.8274 (mm) REVERT: A 491 ARG cc_start: 0.8578 (tpp80) cc_final: 0.8299 (ttm-80) REVERT: A 499 ARG cc_start: 0.8251 (mtp-110) cc_final: 0.7891 (ttp80) REVERT: A 588 LYS cc_start: 0.8243 (tppt) cc_final: 0.7897 (tppt) REVERT: A 598 PHE cc_start: 0.8802 (t80) cc_final: 0.8253 (t80) REVERT: A 609 ARG cc_start: 0.7994 (mmm-85) cc_final: 0.7666 (mmm-85) REVERT: A 613 GLN cc_start: 0.8081 (tt0) cc_final: 0.7874 (tm-30) REVERT: A 616 GLU cc_start: 0.7560 (pt0) cc_final: 0.7266 (pt0) REVERT: A 621 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 633 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8446 (mmtt) REVERT: A 644 LEU cc_start: 0.8517 (mt) cc_final: 0.8298 (mp) REVERT: A 671 MET cc_start: 0.6245 (mmt) cc_final: 0.5666 (mmt) REVERT: A 678 MET cc_start: 0.6595 (ppp) cc_final: 0.6291 (ppp) REVERT: A 697 MET cc_start: 0.6970 (mmm) cc_final: 0.6268 (mmm) REVERT: A 837 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8196 (t80) REVERT: A 868 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8112 (mtpp) REVERT: A 900 GLN cc_start: 0.8272 (mm-40) cc_final: 0.8048 (mm110) REVERT: A 926 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 928 HIS cc_start: 0.7687 (t-90) cc_final: 0.7469 (t-170) REVERT: A 981 HIS cc_start: 0.8027 (m90) cc_final: 0.7721 (m-70) REVERT: A 993 ASP cc_start: 0.7385 (p0) cc_final: 0.7173 (p0) REVERT: A 1033 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 1044 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7801 (mt-10) REVERT: A 1066 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: A 1075 ILE cc_start: 0.8340 (mm) cc_final: 0.8115 (mm) REVERT: A 1087 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 1110 GLN cc_start: 0.7576 (mp10) cc_final: 0.7132 (mp-120) REVERT: A 1122 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 1190 ARG cc_start: 0.7438 (tpt170) cc_final: 0.7079 (mmt180) outliers start: 37 outliers final: 14 residues processed: 293 average time/residue: 0.2355 time to fit residues: 90.8966 Evaluate side-chains 273 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118812 restraints weight = 12518.030| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.99 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8395 Z= 0.217 Angle : 0.574 13.232 11384 Z= 0.297 Chirality : 0.040 0.174 1368 Planarity : 0.004 0.039 1404 Dihedral : 6.146 56.306 1132 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.56 % Allowed : 18.49 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1032 helix: 1.24 (0.19), residues: 763 sheet: 0.28 (0.81), residues: 38 loop : -1.38 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.003 0.000 HIS A 614 PHE 0.027 0.001 PHE A 766 TYR 0.013 0.001 TYR A1035 ARG 0.012 0.001 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8281 (p) cc_final: 0.7989 (m) REVERT: A 149 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 154 MET cc_start: 0.8520 (tpp) cc_final: 0.7219 (tpp) REVERT: A 155 ASP cc_start: 0.7967 (t0) cc_final: 0.7652 (t0) REVERT: A 176 VAL cc_start: 0.8554 (p) cc_final: 0.8288 (t) REVERT: A 190 ASN cc_start: 0.8209 (p0) cc_final: 0.7966 (p0) REVERT: A 197 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 206 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8194 (t) REVERT: A 231 GLU cc_start: 0.7469 (tt0) cc_final: 0.6957 (tt0) REVERT: A 233 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 246 ASN cc_start: 0.8308 (m-40) cc_final: 0.7973 (m110) REVERT: A 338 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8357 (mtmm) REVERT: A 375 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8100 (ttmm) REVERT: A 377 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 386 PHE cc_start: 0.8061 (t80) cc_final: 0.7531 (t80) REVERT: A 412 ARG cc_start: 0.6975 (mtm180) cc_final: 0.6564 (mtm-85) REVERT: A 491 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8298 (ttm-80) REVERT: A 516 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8064 (ttt90) REVERT: A 524 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: A 573 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6646 (mmm160) REVERT: A 588 LYS cc_start: 0.8177 (tppt) cc_final: 0.7906 (tppt) REVERT: A 598 PHE cc_start: 0.8758 (t80) cc_final: 0.8401 (t80) REVERT: A 609 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7465 (mmm-85) REVERT: A 616 GLU cc_start: 0.7553 (pt0) cc_final: 0.7264 (pt0) REVERT: A 621 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: A 633 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8433 (mmtt) REVERT: A 644 LEU cc_start: 0.8530 (mt) cc_final: 0.8304 (mp) REVERT: A 678 MET cc_start: 0.6587 (ppp) cc_final: 0.6237 (ppp) REVERT: A 685 ASN cc_start: 0.8604 (m-40) cc_final: 0.8131 (m-40) REVERT: A 697 MET cc_start: 0.6784 (mmm) cc_final: 0.6582 (mmm) REVERT: A 727 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8054 (ptpp) REVERT: A 824 VAL cc_start: 0.8648 (t) cc_final: 0.8303 (m) REVERT: A 831 ASN cc_start: 0.8067 (m-40) cc_final: 0.7841 (m110) REVERT: A 837 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8175 (t80) REVERT: A 868 LYS cc_start: 0.8297 (mtpp) cc_final: 0.8072 (mtpp) REVERT: A 886 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7923 (tt0) REVERT: A 900 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8048 (mm110) REVERT: A 926 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 981 HIS cc_start: 0.7980 (m90) cc_final: 0.7772 (m-70) REVERT: A 1044 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 1066 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: A 1072 ASP cc_start: 0.7870 (m-30) cc_final: 0.7609 (t0) REVERT: A 1107 MET cc_start: 0.8137 (ttm) cc_final: 0.7935 (ttp) REVERT: A 1110 GLN cc_start: 0.7669 (mp10) cc_final: 0.7254 (mp-120) REVERT: A 1122 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 1139 ASP cc_start: 0.7543 (m-30) cc_final: 0.7287 (m-30) REVERT: A 1190 ARG cc_start: 0.7403 (tpt170) cc_final: 0.7101 (mmt180) outliers start: 32 outliers final: 17 residues processed: 274 average time/residue: 0.2209 time to fit residues: 79.6213 Evaluate side-chains 267 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 86 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1040 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119400 restraints weight = 12379.994| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.97 r_work: 0.3386 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8395 Z= 0.191 Angle : 0.568 13.577 11384 Z= 0.290 Chirality : 0.039 0.168 1368 Planarity : 0.004 0.035 1404 Dihedral : 6.050 56.778 1132 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.67 % Allowed : 20.04 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1032 helix: 1.43 (0.19), residues: 760 sheet: 0.53 (0.81), residues: 38 loop : -1.27 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.000 HIS A 908 PHE 0.027 0.001 PHE A 766 TYR 0.009 0.001 TYR A1153 ARG 0.005 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8260 (p) cc_final: 0.7964 (m) REVERT: A 120 VAL cc_start: 0.7692 (t) cc_final: 0.7398 (m) REVERT: A 129 ASP cc_start: 0.5926 (OUTLIER) cc_final: 0.5677 (p0) REVERT: A 149 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 154 MET cc_start: 0.8477 (tpp) cc_final: 0.7201 (tpp) REVERT: A 155 ASP cc_start: 0.7983 (t0) cc_final: 0.7642 (t0) REVERT: A 176 VAL cc_start: 0.8514 (p) cc_final: 0.8225 (t) REVERT: A 190 ASN cc_start: 0.8237 (p0) cc_final: 0.8010 (p0) REVERT: A 197 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7843 (mt-10) REVERT: A 206 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 231 GLU cc_start: 0.7459 (tt0) cc_final: 0.6942 (tt0) REVERT: A 233 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7598 (tm-30) REVERT: A 246 ASN cc_start: 0.8288 (m-40) cc_final: 0.7910 (m110) REVERT: A 277 LEU cc_start: 0.8535 (mm) cc_final: 0.8293 (mp) REVERT: A 338 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8365 (mtmm) REVERT: A 375 LYS cc_start: 0.8310 (ttpt) cc_final: 0.8085 (ttmm) REVERT: A 377 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 386 PHE cc_start: 0.8006 (t80) cc_final: 0.7553 (t80) REVERT: A 491 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8309 (ttm-80) REVERT: A 499 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7750 (ttp80) REVERT: A 524 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7603 (m-30) REVERT: A 573 ARG cc_start: 0.7276 (mmm160) cc_final: 0.6629 (mmm160) REVERT: A 588 LYS cc_start: 0.8143 (tppt) cc_final: 0.7880 (tppt) REVERT: A 598 PHE cc_start: 0.8741 (t80) cc_final: 0.8348 (t80) REVERT: A 609 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: A 616 GLU cc_start: 0.7572 (pt0) cc_final: 0.7281 (pt0) REVERT: A 621 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 633 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8399 (mmtt) REVERT: A 637 ILE cc_start: 0.8389 (tp) cc_final: 0.8122 (tp) REVERT: A 678 MET cc_start: 0.6519 (ppp) cc_final: 0.6154 (ppp) REVERT: A 685 ASN cc_start: 0.8598 (m-40) cc_final: 0.8203 (m-40) REVERT: A 697 MET cc_start: 0.6833 (mmm) cc_final: 0.6478 (mmm) REVERT: A 824 VAL cc_start: 0.8640 (t) cc_final: 0.8283 (m) REVERT: A 831 ASN cc_start: 0.8017 (m-40) cc_final: 0.7785 (m110) REVERT: A 837 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8191 (t80) REVERT: A 868 LYS cc_start: 0.8303 (mtpp) cc_final: 0.8030 (mtpp) REVERT: A 911 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 926 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 981 HIS cc_start: 0.7941 (m90) cc_final: 0.7740 (m-70) REVERT: A 994 GLU cc_start: 0.8182 (pm20) cc_final: 0.7851 (pm20) REVERT: A 1044 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 1066 TYR cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 1110 GLN cc_start: 0.7719 (mp10) cc_final: 0.7271 (mp-120) REVERT: A 1115 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: A 1122 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 1174 LEU cc_start: 0.7512 (mt) cc_final: 0.7289 (mp) REVERT: A 1190 ARG cc_start: 0.7330 (tpt170) cc_final: 0.7070 (mmt180) outliers start: 33 outliers final: 14 residues processed: 272 average time/residue: 0.2316 time to fit residues: 82.3660 Evaluate side-chains 272 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 98 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A1074 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 = 0.3760 r_free = 0.3760 target = 0.137816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119592 restraints weight = 12394.248| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.97 r_work: 0.3391 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8395 Z= 0.190 Angle : 0.567 13.729 11384 Z= 0.288 Chirality : 0.040 0.175 1368 Planarity : 0.004 0.034 1404 Dihedral : 6.045 59.584 1132 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.34 % Allowed : 21.83 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1032 helix: 1.49 (0.19), residues: 760 sheet: 0.59 (0.81), residues: 38 loop : -1.19 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.028 0.001 PHE A 766 TYR 0.008 0.001 TYR A 309 ARG 0.005 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8244 (p) cc_final: 0.7944 (m) REVERT: A 120 VAL cc_start: 0.7726 (t) cc_final: 0.7410 (m) REVERT: A 149 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 154 MET cc_start: 0.8462 (tpp) cc_final: 0.7599 (tpp) REVERT: A 155 ASP cc_start: 0.8008 (t0) cc_final: 0.7679 (t0) REVERT: A 176 VAL cc_start: 0.8498 (p) cc_final: 0.8237 (t) REVERT: A 190 ASN cc_start: 0.8248 (p0) cc_final: 0.8000 (p0) REVERT: A 197 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 206 SER cc_start: 0.8603 (m) cc_final: 0.8178 (t) REVERT: A 217 LEU cc_start: 0.8643 (mt) cc_final: 0.8324 (mm) REVERT: A 231 GLU cc_start: 0.7475 (tt0) cc_final: 0.7271 (tt0) REVERT: A 233 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7592 (tm-30) REVERT: A 246 ASN cc_start: 0.8270 (m-40) cc_final: 0.7935 (m110) REVERT: A 277 LEU cc_start: 0.8538 (mm) cc_final: 0.8287 (mp) REVERT: A 377 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 386 PHE cc_start: 0.7991 (t80) cc_final: 0.7529 (t80) REVERT: A 387 TYR cc_start: 0.8303 (m-10) cc_final: 0.8094 (m-10) REVERT: A 412 ARG cc_start: 0.7205 (mtm180) cc_final: 0.6976 (mtm180) REVERT: A 465 LEU cc_start: 0.8465 (mt) cc_final: 0.8223 (mp) REVERT: A 477 LEU cc_start: 0.8517 (tp) cc_final: 0.8286 (tp) REVERT: A 491 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8302 (ttm-80) REVERT: A 516 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8076 (ttt90) REVERT: A 524 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7600 (m-30) REVERT: A 573 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6576 (mmm160) REVERT: A 588 LYS cc_start: 0.8101 (tppt) cc_final: 0.7845 (tppt) REVERT: A 598 PHE cc_start: 0.8704 (t80) cc_final: 0.8168 (t80) REVERT: A 606 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: A 609 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7433 (mmm-85) REVERT: A 616 GLU cc_start: 0.7553 (pt0) cc_final: 0.7269 (pt0) REVERT: A 621 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 633 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8391 (mmtt) REVERT: A 637 ILE cc_start: 0.8397 (tp) cc_final: 0.8130 (tp) REVERT: A 678 MET cc_start: 0.6523 (ppp) cc_final: 0.6147 (ppp) REVERT: A 685 ASN cc_start: 0.8594 (m-40) cc_final: 0.8156 (m-40) REVERT: A 697 MET cc_start: 0.6333 (mmm) cc_final: 0.6124 (mmm) REVERT: A 824 VAL cc_start: 0.8618 (t) cc_final: 0.8263 (m) REVERT: A 831 ASN cc_start: 0.8025 (m-40) cc_final: 0.7769 (m110) REVERT: A 837 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.8139 (t80) REVERT: A 868 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8004 (mtpp) REVERT: A 876 LEU cc_start: 0.8474 (mt) cc_final: 0.8135 (mp) REVERT: A 911 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 926 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 940 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7807 (mtt90) REVERT: A 981 HIS cc_start: 0.7926 (m90) cc_final: 0.7606 (m90) REVERT: A 994 GLU cc_start: 0.8209 (pm20) cc_final: 0.7897 (pm20) REVERT: A 999 PHE cc_start: 0.7653 (m-10) cc_final: 0.7448 (m-10) REVERT: A 1044 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 1066 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: A 1110 GLN cc_start: 0.7745 (mp10) cc_final: 0.7272 (mp-120) REVERT: A 1115 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: A 1122 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 1174 LEU cc_start: 0.7488 (mt) cc_final: 0.7266 (mp) REVERT: A 1190 ARG cc_start: 0.7324 (tpt170) cc_final: 0.7052 (mmt180) outliers start: 30 outliers final: 18 residues processed: 272 average time/residue: 0.2387 time to fit residues: 85.4142 Evaluate side-chains 286 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A1074 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 = 0.3748 r_free = 0.3748 target = 0.137064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.118994 restraints weight = 12411.437| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.97 r_work: 0.3381 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8395 Z= 0.222 Angle : 0.582 14.076 11384 Z= 0.298 Chirality : 0.040 0.168 1368 Planarity : 0.004 0.034 1404 Dihedral : 6.051 58.886 1132 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.67 % Allowed : 21.83 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1032 helix: 1.52 (0.19), residues: 760 sheet: 0.64 (0.80), residues: 38 loop : -1.19 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.024 0.001 PHE A 766 TYR 0.010 0.001 TYR A 309 ARG 0.006 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8234 (p) cc_final: 0.7929 (m) REVERT: A 120 VAL cc_start: 0.7763 (t) cc_final: 0.7469 (m) REVERT: A 149 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 154 MET cc_start: 0.8472 (tpp) cc_final: 0.7659 (tpp) REVERT: A 155 ASP cc_start: 0.8028 (t0) cc_final: 0.7691 (t0) REVERT: A 176 VAL cc_start: 0.8535 (p) cc_final: 0.8297 (t) REVERT: A 190 ASN cc_start: 0.8238 (p0) cc_final: 0.8008 (p0) REVERT: A 197 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 206 SER cc_start: 0.8623 (m) cc_final: 0.8176 (t) REVERT: A 217 LEU cc_start: 0.8645 (mt) cc_final: 0.8316 (mm) REVERT: A 231 GLU cc_start: 0.7508 (tt0) cc_final: 0.7294 (tt0) REVERT: A 233 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 246 ASN cc_start: 0.8268 (m-40) cc_final: 0.7936 (m110) REVERT: A 277 LEU cc_start: 0.8554 (mm) cc_final: 0.8293 (mp) REVERT: A 377 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 386 PHE cc_start: 0.8013 (t80) cc_final: 0.7551 (t80) REVERT: A 387 TYR cc_start: 0.8306 (m-10) cc_final: 0.8055 (m-10) REVERT: A 412 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6979 (mtm180) REVERT: A 465 LEU cc_start: 0.8461 (mt) cc_final: 0.8218 (mp) REVERT: A 477 LEU cc_start: 0.8558 (tp) cc_final: 0.8313 (tp) REVERT: A 491 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8295 (ttm-80) REVERT: A 516 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8049 (ttt90) REVERT: A 524 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: A 573 ARG cc_start: 0.7317 (mmm160) cc_final: 0.6553 (mmm160) REVERT: A 588 LYS cc_start: 0.8128 (tppt) cc_final: 0.7858 (tppt) REVERT: A 598 PHE cc_start: 0.8698 (t80) cc_final: 0.8149 (t80) REVERT: A 606 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 609 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: A 616 GLU cc_start: 0.7575 (pt0) cc_final: 0.7290 (pt0) REVERT: A 621 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 633 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8408 (mmtt) REVERT: A 637 ILE cc_start: 0.8459 (tp) cc_final: 0.8176 (tp) REVERT: A 651 LEU cc_start: 0.8780 (tt) cc_final: 0.8374 (tp) REVERT: A 678 MET cc_start: 0.6582 (ppp) cc_final: 0.6193 (ppp) REVERT: A 685 ASN cc_start: 0.8589 (m-40) cc_final: 0.8163 (m-40) REVERT: A 756 ARG cc_start: 0.7538 (mmp80) cc_final: 0.6421 (pmt170) REVERT: A 773 VAL cc_start: 0.8289 (t) cc_final: 0.8072 (p) REVERT: A 824 VAL cc_start: 0.8627 (t) cc_final: 0.8261 (m) REVERT: A 831 ASN cc_start: 0.8053 (m-40) cc_final: 0.7794 (m110) REVERT: A 835 LEU cc_start: 0.8700 (tp) cc_final: 0.8452 (tt) REVERT: A 837 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8098 (t80) REVERT: A 868 LYS cc_start: 0.8193 (mtpp) cc_final: 0.7916 (mtpp) REVERT: A 876 LEU cc_start: 0.8471 (mt) cc_final: 0.8129 (mp) REVERT: A 911 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 926 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 940 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7830 (mtt90) REVERT: A 981 HIS cc_start: 0.7965 (m90) cc_final: 0.7638 (m90) REVERT: A 994 GLU cc_start: 0.8180 (pm20) cc_final: 0.7896 (pm20) REVERT: A 1007 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8347 (ttmt) REVERT: A 1044 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 1066 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 1104 MET cc_start: 0.8238 (ttt) cc_final: 0.7942 (ttp) REVERT: A 1110 GLN cc_start: 0.7787 (mp10) cc_final: 0.7344 (mp-120) REVERT: A 1115 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: A 1122 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 1174 LEU cc_start: 0.7550 (mt) cc_final: 0.7310 (mp) REVERT: A 1190 ARG cc_start: 0.7323 (tpt170) cc_final: 0.7037 (mmt180) outliers start: 33 outliers final: 23 residues processed: 271 average time/residue: 0.2254 time to fit residues: 79.9685 Evaluate side-chains 286 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A1074 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 = 0.3744 r_free = 0.3744 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118696 restraints weight = 12392.852| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.97 r_work: 0.3374 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8395 Z= 0.230 Angle : 0.590 14.072 11384 Z= 0.303 Chirality : 0.041 0.173 1368 Planarity : 0.004 0.033 1404 Dihedral : 6.050 57.115 1132 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.01 % Allowed : 21.71 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1032 helix: 1.52 (0.19), residues: 767 sheet: 0.59 (0.79), residues: 38 loop : -1.28 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 643 HIS 0.004 0.001 HIS A 908 PHE 0.026 0.001 PHE A 766 TYR 0.010 0.001 TYR A 309 ARG 0.006 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8228 (p) cc_final: 0.7922 (m) REVERT: A 120 VAL cc_start: 0.7758 (t) cc_final: 0.7469 (m) REVERT: A 149 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 154 MET cc_start: 0.8473 (tpp) cc_final: 0.7671 (tpp) REVERT: A 155 ASP cc_start: 0.8027 (t0) cc_final: 0.7785 (t0) REVERT: A 176 VAL cc_start: 0.8543 (p) cc_final: 0.8306 (t) REVERT: A 190 ASN cc_start: 0.8247 (p0) cc_final: 0.8023 (p0) REVERT: A 206 SER cc_start: 0.8632 (m) cc_final: 0.8203 (t) REVERT: A 217 LEU cc_start: 0.8649 (mt) cc_final: 0.8314 (mm) REVERT: A 231 GLU cc_start: 0.7514 (tt0) cc_final: 0.7292 (tt0) REVERT: A 233 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7588 (tm-30) REVERT: A 277 LEU cc_start: 0.8566 (mm) cc_final: 0.8306 (mp) REVERT: A 386 PHE cc_start: 0.7991 (t80) cc_final: 0.7533 (t80) REVERT: A 387 TYR cc_start: 0.8314 (m-10) cc_final: 0.8089 (m-10) REVERT: A 412 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6955 (mtm180) REVERT: A 465 LEU cc_start: 0.8453 (mt) cc_final: 0.8214 (mp) REVERT: A 477 LEU cc_start: 0.8598 (tp) cc_final: 0.8350 (tp) REVERT: A 491 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8293 (ttm-80) REVERT: A 516 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8042 (ttt90) REVERT: A 524 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: A 573 ARG cc_start: 0.7345 (mmm160) cc_final: 0.6582 (mmm160) REVERT: A 588 LYS cc_start: 0.8098 (tppt) cc_final: 0.7842 (tppt) REVERT: A 598 PHE cc_start: 0.8685 (t80) cc_final: 0.8187 (t80) REVERT: A 606 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: A 609 ARG cc_start: 0.7640 (mmm-85) cc_final: 0.7397 (mmm-85) REVERT: A 616 GLU cc_start: 0.7571 (pt0) cc_final: 0.7296 (pt0) REVERT: A 621 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 633 LYS cc_start: 0.8669 (mmtt) cc_final: 0.8403 (mmtt) REVERT: A 637 ILE cc_start: 0.8578 (tp) cc_final: 0.8297 (tp) REVERT: A 678 MET cc_start: 0.6614 (ppp) cc_final: 0.6225 (ppp) REVERT: A 685 ASN cc_start: 0.8554 (m-40) cc_final: 0.8149 (m-40) REVERT: A 756 ARG cc_start: 0.7355 (mmp80) cc_final: 0.6260 (ppt170) REVERT: A 773 VAL cc_start: 0.8277 (t) cc_final: 0.8059 (p) REVERT: A 824 VAL cc_start: 0.8618 (t) cc_final: 0.8257 (m) REVERT: A 831 ASN cc_start: 0.8057 (m-40) cc_final: 0.7788 (m110) REVERT: A 837 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8051 (t80) REVERT: A 868 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7941 (mtpp) REVERT: A 876 LEU cc_start: 0.8441 (mt) cc_final: 0.8097 (mp) REVERT: A 911 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 926 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 981 HIS cc_start: 0.8006 (m90) cc_final: 0.7797 (m-70) REVERT: A 994 GLU cc_start: 0.8214 (pm20) cc_final: 0.7799 (pm20) REVERT: A 1007 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8352 (ttmt) REVERT: A 1044 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 1066 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: A 1110 GLN cc_start: 0.7814 (mp10) cc_final: 0.7361 (mp-120) REVERT: A 1122 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7541 (mm-30) REVERT: A 1174 LEU cc_start: 0.7559 (mt) cc_final: 0.7343 (mp) REVERT: A 1190 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6996 (mmt180) outliers start: 36 outliers final: 24 residues processed: 273 average time/residue: 0.2320 time to fit residues: 83.0335 Evaluate side-chains 275 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 GLN Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A1074 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 = 0.3756 r_free = 0.3756 target = 0.137649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119618 restraints weight = 12476.528| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.99 r_work: 0.3390 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8395 Z= 0.193 Angle : 0.594 13.862 11384 Z= 0.301 Chirality : 0.040 0.187 1368 Planarity : 0.004 0.033 1404 Dihedral : 5.755 57.661 1130 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.12 % Allowed : 22.05 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.27), residues: 1032 helix: 1.60 (0.19), residues: 767 sheet: 0.71 (0.79), residues: 38 loop : -1.21 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.000 HIS A 908 PHE 0.026 0.001 PHE A 766 TYR 0.008 0.001 TYR A 309 ARG 0.006 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8184 (p) cc_final: 0.7883 (m) REVERT: A 120 VAL cc_start: 0.7734 (t) cc_final: 0.7446 (m) REVERT: A 149 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 154 MET cc_start: 0.8430 (tpp) cc_final: 0.7643 (tpp) REVERT: A 155 ASP cc_start: 0.8059 (t0) cc_final: 0.7548 (t0) REVERT: A 176 VAL cc_start: 0.8535 (p) cc_final: 0.8279 (t) REVERT: A 190 ASN cc_start: 0.8209 (p0) cc_final: 0.7995 (p0) REVERT: A 206 SER cc_start: 0.8638 (m) cc_final: 0.8168 (t) REVERT: A 217 LEU cc_start: 0.8666 (mt) cc_final: 0.8334 (mm) REVERT: A 231 GLU cc_start: 0.7512 (tt0) cc_final: 0.7280 (tt0) REVERT: A 233 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 277 LEU cc_start: 0.8563 (mm) cc_final: 0.8305 (mp) REVERT: A 286 THR cc_start: 0.8610 (m) cc_final: 0.8336 (p) REVERT: A 386 PHE cc_start: 0.7960 (t80) cc_final: 0.7517 (t80) REVERT: A 412 ARG cc_start: 0.7235 (mtm180) cc_final: 0.6939 (mtm180) REVERT: A 465 LEU cc_start: 0.8428 (mt) cc_final: 0.8182 (mp) REVERT: A 477 LEU cc_start: 0.8575 (tp) cc_final: 0.8307 (tp) REVERT: A 491 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8278 (ttm-80) REVERT: A 516 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.8031 (ttt90) REVERT: A 524 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: A 573 ARG cc_start: 0.7320 (mmm160) cc_final: 0.6547 (mmm160) REVERT: A 588 LYS cc_start: 0.8053 (tppt) cc_final: 0.7801 (tppt) REVERT: A 598 PHE cc_start: 0.8684 (t80) cc_final: 0.8199 (t80) REVERT: A 606 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: A 609 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7372 (mmm-85) REVERT: A 616 GLU cc_start: 0.7538 (pt0) cc_final: 0.7256 (pt0) REVERT: A 621 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: A 633 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8357 (mmtt) REVERT: A 637 ILE cc_start: 0.8485 (tp) cc_final: 0.8199 (tp) REVERT: A 678 MET cc_start: 0.6562 (ppp) cc_final: 0.6184 (ppp) REVERT: A 685 ASN cc_start: 0.8495 (m-40) cc_final: 0.8108 (m-40) REVERT: A 756 ARG cc_start: 0.7345 (mmp80) cc_final: 0.6215 (ppt170) REVERT: A 773 VAL cc_start: 0.8268 (t) cc_final: 0.8063 (p) REVERT: A 824 VAL cc_start: 0.8624 (t) cc_final: 0.8255 (m) REVERT: A 831 ASN cc_start: 0.8012 (m-40) cc_final: 0.7759 (m110) REVERT: A 835 LEU cc_start: 0.8634 (tt) cc_final: 0.8315 (tp) REVERT: A 837 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8075 (t80) REVERT: A 847 GLU cc_start: 0.8015 (tp30) cc_final: 0.7764 (tp30) REVERT: A 876 LEU cc_start: 0.8444 (mt) cc_final: 0.8111 (mp) REVERT: A 911 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 926 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 981 HIS cc_start: 0.7912 (m90) cc_final: 0.7565 (m90) REVERT: A 994 GLU cc_start: 0.8199 (pm20) cc_final: 0.7787 (pm20) REVERT: A 1007 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8258 (ttmm) REVERT: A 1044 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 1066 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: A 1104 MET cc_start: 0.8220 (mtp) cc_final: 0.7914 (ttt) REVERT: A 1110 GLN cc_start: 0.7819 (mp10) cc_final: 0.7354 (mp-120) REVERT: A 1122 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 1174 LEU cc_start: 0.7526 (mt) cc_final: 0.7303 (mp) outliers start: 37 outliers final: 26 residues processed: 270 average time/residue: 0.2250 time to fit residues: 79.9707 Evaluate side-chains 278 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A1074 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 = 0.3744 r_free = 0.3744 target = 0.136563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118726 restraints weight = 12621.547| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.99 r_work: 0.3380 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8395 Z= 0.236 Angle : 0.617 14.310 11384 Z= 0.314 Chirality : 0.041 0.187 1368 Planarity : 0.004 0.032 1404 Dihedral : 5.812 58.651 1130 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.67 % Allowed : 22.49 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1032 helix: 1.54 (0.19), residues: 767 sheet: 0.67 (0.79), residues: 38 loop : -1.20 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.027 0.001 PHE A 766 TYR 0.016 0.001 TYR A 387 ARG 0.007 0.000 ARG A1162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8229 (p) cc_final: 0.7925 (m) REVERT: A 120 VAL cc_start: 0.7764 (t) cc_final: 0.7472 (m) REVERT: A 149 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 154 MET cc_start: 0.8482 (tpp) cc_final: 0.7670 (tpp) REVERT: A 176 VAL cc_start: 0.8557 (p) cc_final: 0.8317 (t) REVERT: A 190 ASN cc_start: 0.8221 (p0) cc_final: 0.8015 (p0) REVERT: A 206 SER cc_start: 0.8632 (m) cc_final: 0.8147 (t) REVERT: A 217 LEU cc_start: 0.8664 (mt) cc_final: 0.8319 (mm) REVERT: A 231 GLU cc_start: 0.7495 (tt0) cc_final: 0.7273 (tt0) REVERT: A 233 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 277 LEU cc_start: 0.8576 (mm) cc_final: 0.8314 (mp) REVERT: A 338 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8321 (mtmm) REVERT: A 386 PHE cc_start: 0.7980 (t80) cc_final: 0.7527 (t80) REVERT: A 412 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6986 (mtm180) REVERT: A 477 LEU cc_start: 0.8597 (tp) cc_final: 0.8336 (tp) REVERT: A 491 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8277 (ttm-80) REVERT: A 516 ARG cc_start: 0.8285 (ttm-80) cc_final: 0.7977 (ttt90) REVERT: A 524 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: A 532 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7884 (mt) REVERT: A 573 ARG cc_start: 0.7319 (mmm160) cc_final: 0.6545 (mmm160) REVERT: A 588 LYS cc_start: 0.8073 (tppt) cc_final: 0.7822 (tppt) REVERT: A 598 PHE cc_start: 0.8694 (t80) cc_final: 0.8169 (t80) REVERT: A 606 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7581 (pm20) REVERT: A 609 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7358 (mmm-85) REVERT: A 616 GLU cc_start: 0.7557 (pt0) cc_final: 0.7275 (pt0) REVERT: A 621 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 633 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8353 (mmtt) REVERT: A 671 MET cc_start: 0.6632 (mmt) cc_final: 0.6190 (mmt) REVERT: A 678 MET cc_start: 0.6644 (ppp) cc_final: 0.6258 (ppp) REVERT: A 685 ASN cc_start: 0.8498 (m-40) cc_final: 0.8212 (m-40) REVERT: A 698 GLU cc_start: 0.7874 (pp20) cc_final: 0.7571 (tm-30) REVERT: A 756 ARG cc_start: 0.7364 (mmp80) cc_final: 0.6161 (ppt170) REVERT: A 773 VAL cc_start: 0.8264 (t) cc_final: 0.8060 (p) REVERT: A 824 VAL cc_start: 0.8614 (t) cc_final: 0.8253 (m) REVERT: A 831 ASN cc_start: 0.8055 (m-40) cc_final: 0.7795 (m110) REVERT: A 837 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 876 LEU cc_start: 0.8424 (mt) cc_final: 0.8083 (mp) REVERT: A 881 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7923 (mt-10) REVERT: A 911 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7725 (mt-10) REVERT: A 926 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7274 (mm-30) REVERT: A 981 HIS cc_start: 0.7959 (m90) cc_final: 0.7740 (m-70) REVERT: A 994 GLU cc_start: 0.8204 (pm20) cc_final: 0.7791 (pm20) REVERT: A 1007 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8284 (ttmm) REVERT: A 1044 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7740 (mt-10) REVERT: A 1066 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: A 1104 MET cc_start: 0.8238 (mtp) cc_final: 0.7948 (ttt) REVERT: A 1110 GLN cc_start: 0.7847 (mp10) cc_final: 0.7383 (mp-120) REVERT: A 1122 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 1162 ARG cc_start: 0.6375 (ttp80) cc_final: 0.6164 (ttp80) REVERT: A 1174 LEU cc_start: 0.7393 (mt) cc_final: 0.7173 (mp) outliers start: 33 outliers final: 22 residues processed: 267 average time/residue: 0.2395 time to fit residues: 84.2089 Evaluate side-chains 272 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119288 restraints weight = 12375.952| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.98 r_work: 0.3389 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8395 Z= 0.212 Angle : 0.616 14.109 11384 Z= 0.313 Chirality : 0.041 0.254 1368 Planarity : 0.004 0.032 1404 Dihedral : 5.715 59.213 1128 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.56 % Allowed : 23.05 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1032 helix: 1.58 (0.19), residues: 767 sheet: 0.72 (0.79), residues: 38 loop : -1.19 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.028 0.001 PHE A 766 TYR 0.009 0.001 TYR A 309 ARG 0.007 0.000 ARG A1162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2064 Ramachandran restraints generated. 1032 Oldfield, 0 Emsley, 1032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8192 (p) cc_final: 0.7892 (m) REVERT: A 120 VAL cc_start: 0.7757 (t) cc_final: 0.7480 (m) REVERT: A 149 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 154 MET cc_start: 0.8476 (tpp) cc_final: 0.7644 (tpp) REVERT: A 176 VAL cc_start: 0.8541 (p) cc_final: 0.8286 (t) REVERT: A 190 ASN cc_start: 0.8203 (p0) cc_final: 0.7967 (p0) REVERT: A 206 SER cc_start: 0.8634 (m) cc_final: 0.8151 (t) REVERT: A 217 LEU cc_start: 0.8659 (mt) cc_final: 0.8321 (mm) REVERT: A 231 GLU cc_start: 0.7480 (tt0) cc_final: 0.7267 (tt0) REVERT: A 233 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 277 LEU cc_start: 0.8588 (mm) cc_final: 0.8321 (mp) REVERT: A 286 THR cc_start: 0.8610 (m) cc_final: 0.8321 (p) REVERT: A 303 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 338 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8341 (mtmm) REVERT: A 386 PHE cc_start: 0.7954 (t80) cc_final: 0.7526 (t80) REVERT: A 412 ARG cc_start: 0.7273 (mtm180) cc_final: 0.6976 (mtm180) REVERT: A 477 LEU cc_start: 0.8570 (tp) cc_final: 0.8297 (tp) REVERT: A 491 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8252 (ttm-80) REVERT: A 516 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8023 (ttt90) REVERT: A 524 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: A 573 ARG cc_start: 0.7290 (mmm160) cc_final: 0.6501 (mmm160) REVERT: A 588 LYS cc_start: 0.8066 (tppt) cc_final: 0.7814 (tppt) REVERT: A 598 PHE cc_start: 0.8686 (t80) cc_final: 0.8166 (t80) REVERT: A 609 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: A 616 GLU cc_start: 0.7534 (pt0) cc_final: 0.7250 (pt0) REVERT: A 621 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 633 LYS cc_start: 0.8684 (mmtt) cc_final: 0.8342 (mmtt) REVERT: A 671 MET cc_start: 0.6627 (mmt) cc_final: 0.6159 (mmt) REVERT: A 678 MET cc_start: 0.6627 (ppp) cc_final: 0.6242 (ppp) REVERT: A 685 ASN cc_start: 0.8459 (m-40) cc_final: 0.8173 (m-40) REVERT: A 698 GLU cc_start: 0.7870 (pp20) cc_final: 0.7470 (tm-30) REVERT: A 756 ARG cc_start: 0.7434 (mmp80) cc_final: 0.6262 (ppt170) REVERT: A 824 VAL cc_start: 0.8608 (t) cc_final: 0.8242 (m) REVERT: A 831 ASN cc_start: 0.8020 (m-40) cc_final: 0.7745 (m110) REVERT: A 832 GLN cc_start: 0.8107 (tt0) cc_final: 0.7780 (tp-100) REVERT: A 837 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.8157 (t80) REVERT: A 876 LEU cc_start: 0.8419 (mt) cc_final: 0.8073 (mp) REVERT: A 911 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 926 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 981 HIS cc_start: 0.7947 (m90) cc_final: 0.7742 (m-70) REVERT: A 994 GLU cc_start: 0.8192 (pm20) cc_final: 0.7767 (pm20) REVERT: A 1007 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8264 (ttmm) REVERT: A 1044 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 1066 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: A 1104 MET cc_start: 0.8230 (mtp) cc_final: 0.7929 (ttt) REVERT: A 1110 GLN cc_start: 0.7849 (mp10) cc_final: 0.7383 (mp-120) REVERT: A 1122 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 1162 ARG cc_start: 0.6393 (ttp80) cc_final: 0.6186 (ttp80) REVERT: A 1174 LEU cc_start: 0.7334 (mt) cc_final: 0.7092 (mp) outliers start: 32 outliers final: 22 residues processed: 261 average time/residue: 0.2275 time to fit residues: 78.1250 Evaluate side-chains 271 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 GLU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1007 LYS Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1161 ILE Chi-restraints excluded: chain A residue 1179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A1074 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 = 0.3747 r_free = 0.3747 target = 0.136662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118991 restraints weight = 12511.875| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.97 r_work: 0.3383 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8395 Z= 0.239 Angle : 0.636 14.449 11384 Z= 0.321 Chirality : 0.042 0.205 1368 Planarity : 0.004 0.044 1404 Dihedral : 5.792 59.995 1128 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.34 % Allowed : 23.94 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1032 helix: 1.54 (0.19), residues: 768 sheet: 0.70 (0.77), residues: 38 loop : -1.33 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 PHE 0.031 0.002 PHE A 999 TYR 0.010 0.001 TYR A 309 ARG 0.006 0.000 ARG A1162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4812.56 seconds wall clock time: 83 minutes 43.43 seconds (5023.43 seconds total)