Starting phenix.real_space_refine on Fri Aug 22 22:13:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xq4_38565/08_2025/8xq4_38565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xq4_38565/08_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_38565/08_2025/8xq4_38565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xq4_38565/08_2025/8xq4_38565.map" model { file = "/net/cci-nas-00/data/ceres_data/8xq4_38565/08_2025/8xq4_38565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xq4_38565/08_2025/8xq4_38565.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.95, per 1000 atoms: 0.24 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: 0.57 Conformation dependent library (CDL) restraints added in 485.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 1.97 Time building geometry restraints manager: 0.83 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- 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= 0.187 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 : 3.63 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (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 ARG 0.001 0.000 ARG A 887 TYR 0.010 0.001 TYR A 191 PHE 0.043 0.001 PHE A 766 TRP 0.012 0.001 TRP A 635 HIS 0.002 0.000 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8395) covalent geometry : angle 0.73727 (11384) hydrogen bonds : bond 0.10287 ( 618) hydrogen bonds : angle 5.75074 ( 1833) *********************** 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 : 0.308 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: 0.7511 (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: 0.7796 (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: 0.7563 (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: 0.7378 (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: 0.7279 (tt0) REVERT: A 233 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 237 ASN cc_start: 0.8043 (t0) cc_final: 0.7836 (t0) REVERT: A 246 ASN cc_start: 0.8281 (m-40) cc_final: 0.7998 (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: 0.7530 (t80) REVERT: A 406 PHE cc_start: 0.7995 (m-80) cc_final: 0.7789 (m-10) REVERT: A 491 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8262 (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: 0.7698 (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: 0.7333 (mp0) REVERT: A 633 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8482 (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: 0.0982 time to fit residues: 41.9990 Evaluate side-chains 283 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 268 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 165 GLN A 295 ASN A1040 ASN ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117253 restraints weight = 12710.832| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.06 r_work: 0.3357 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8395 Z= 0.183 Angle : 0.593 14.425 11384 Z= 0.307 Chirality : 0.040 0.180 1368 Planarity : 0.005 0.041 1404 Dihedral : 7.046 58.814 1144 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.23 % Allowed : 15.03 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.26), residues: 1032 helix: 0.82 (0.19), residues: 760 sheet: -0.29 (0.72), residues: 48 loop : -1.48 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 812 TYR 0.009 0.001 TYR A 309 PHE 0.030 0.002 PHE A 766 TRP 0.015 0.002 TRP A1112 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8395) covalent geometry : angle 0.59307 (11384) hydrogen bonds : bond 0.05055 ( 618) hydrogen bonds : angle 4.37490 ( 1833) *********************** 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 314 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8333 (p) cc_final: 0.8030 (m) REVERT: A 112 ILE cc_start: 0.8522 (mm) cc_final: 0.8289 (mm) REVERT: A 137 VAL cc_start: 0.8471 (m) cc_final: 0.8254 (p) REVERT: A 149 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 154 MET cc_start: 0.8529 (tpp) cc_final: 0.6987 (tpp) REVERT: A 155 ASP cc_start: 0.8005 (t0) cc_final: 0.7730 (t0) REVERT: A 163 PHE cc_start: 0.8208 (t80) cc_final: 0.7932 (t80) REVERT: A 174 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8298 (tp) REVERT: A 176 VAL cc_start: 0.8554 (p) cc_final: 0.8281 (t) REVERT: A 190 ASN cc_start: 0.8247 (p0) cc_final: 0.8014 (p0) REVERT: A 197 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 231 GLU cc_start: 0.7461 (tt0) cc_final: 0.6975 (tt0) REVERT: A 233 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7648 (tm-30) REVERT: A 246 ASN cc_start: 0.8224 (m-40) cc_final: 0.7925 (m110) REVERT: A 338 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8366 (mtmm) REVERT: A 375 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8097 (ttmm) REVERT: A 377 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (mp) REVERT: A 386 PHE cc_start: 0.8103 (t80) cc_final: 0.7509 (t80) REVERT: A 480 ILE cc_start: 0.8013 (mt) cc_final: 0.7722 (mt) REVERT: A 486 ILE cc_start: 0.8482 (mp) cc_final: 0.8260 (mm) REVERT: A 491 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8303 (ttm-80) REVERT: A 499 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7898 (ttp80) REVERT: A 588 LYS cc_start: 0.8251 (tppt) cc_final: 0.7906 (tppt) REVERT: A 598 PHE cc_start: 0.8803 (t80) cc_final: 0.8271 (t80) REVERT: A 609 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: A 616 GLU cc_start: 0.7569 (pt0) cc_final: 0.7278 (pt0) REVERT: A 621 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 633 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8462 (mmtt) REVERT: A 644 LEU cc_start: 0.8531 (mt) cc_final: 0.8311 (mp) REVERT: A 671 MET cc_start: 0.6275 (mmt) cc_final: 0.5703 (mmt) REVERT: A 678 MET cc_start: 0.6639 (ppp) cc_final: 0.6321 (ppp) REVERT: A 685 ASN cc_start: 0.8673 (m-40) cc_final: 0.8204 (m-40) REVERT: A 697 MET cc_start: 0.6991 (mmm) cc_final: 0.6266 (mmm) REVERT: A 837 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8238 (t80) REVERT: A 868 LYS cc_start: 0.8270 (mtpp) cc_final: 0.8057 (mtpp) REVERT: A 900 GLN cc_start: 0.8254 (mm-40) cc_final: 0.8034 (mm110) REVERT: A 926 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 981 HIS cc_start: 0.8057 (m90) cc_final: 0.7815 (m-70) REVERT: A 1044 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7809 (mt-10) REVERT: A 1066 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 1075 ILE cc_start: 0.8354 (mm) cc_final: 0.8112 (mm) REVERT: A 1087 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7818 (mm-30) REVERT: A 1110 GLN cc_start: 0.7591 (mp10) cc_final: 0.7155 (mp-120) REVERT: A 1122 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 1144 ASP cc_start: 0.7245 (p0) cc_final: 0.7043 (p0) REVERT: A 1190 ARG cc_start: 0.7452 (tpt170) cc_final: 0.7094 (mmt180) outliers start: 38 outliers final: 14 residues processed: 295 average time/residue: 0.1142 time to fit residues: 44.3875 Evaluate side-chains 270 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 251 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 191 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 371 VAL 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 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 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 57 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.137044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118530 restraints weight = 12284.516| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.97 r_work: 0.3378 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8395 Z= 0.161 Angle : 0.580 13.298 11384 Z= 0.300 Chirality : 0.040 0.170 1368 Planarity : 0.004 0.040 1404 Dihedral : 6.246 56.900 1134 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.23 % Allowed : 18.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.26), residues: 1032 helix: 1.24 (0.19), residues: 759 sheet: 0.28 (0.83), residues: 38 loop : -1.43 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 733 TYR 0.009 0.001 TYR A 309 PHE 0.026 0.001 PHE A 766 TRP 0.012 0.001 TRP A 353 HIS 0.003 0.000 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8395) covalent geometry : angle 0.58001 (11384) hydrogen bonds : bond 0.04845 ( 618) hydrogen bonds : angle 4.26443 ( 1833) *********************** 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 285 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8261 (p) cc_final: 0.7966 (m) REVERT: A 149 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 154 MET cc_start: 0.8513 (tpp) cc_final: 0.7029 (tpp) REVERT: A 155 ASP cc_start: 0.7932 (t0) cc_final: 0.7583 (t0) REVERT: A 176 VAL cc_start: 0.8546 (p) cc_final: 0.8287 (t) REVERT: A 190 ASN cc_start: 0.8207 (p0) cc_final: 0.7960 (p0) REVERT: A 197 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7823 (mt-10) REVERT: A 231 GLU cc_start: 0.7457 (tt0) cc_final: 0.6940 (tt0) REVERT: A 233 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 246 ASN cc_start: 0.8300 (m-40) cc_final: 0.7917 (m110) REVERT: A 338 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8368 (mtmm) REVERT: A 375 LYS cc_start: 0.8320 (ttpt) cc_final: 0.8099 (ttmm) REVERT: A 386 PHE cc_start: 0.8066 (t80) cc_final: 0.7528 (t80) REVERT: A 412 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6595 (mtm-85) REVERT: A 480 ILE cc_start: 0.8032 (mt) cc_final: 0.7759 (mt) REVERT: A 491 ARG cc_start: 0.8589 (tpp80) cc_final: 0.8296 (ttm-80) REVERT: A 499 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7749 (ttp80) REVERT: A 524 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: A 573 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6798 (mmm160) REVERT: A 588 LYS cc_start: 0.8178 (tppt) cc_final: 0.7903 (tppt) REVERT: A 598 PHE cc_start: 0.8755 (t80) cc_final: 0.8408 (t80) REVERT: A 609 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: A 616 GLU cc_start: 0.7506 (pt0) cc_final: 0.7219 (pt0) REVERT: A 621 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: A 633 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8451 (mmtt) REVERT: A 637 ILE cc_start: 0.8442 (tp) cc_final: 0.8070 (tp) REVERT: A 678 MET cc_start: 0.6536 (ppp) cc_final: 0.6191 (ppp) REVERT: A 685 ASN cc_start: 0.8605 (m-40) cc_final: 0.8145 (m-40) REVERT: A 697 MET cc_start: 0.6774 (mmm) cc_final: 0.6517 (mmm) REVERT: A 824 VAL cc_start: 0.8664 (t) cc_final: 0.8317 (m) REVERT: A 831 ASN cc_start: 0.8059 (m-40) cc_final: 0.7832 (m110) REVERT: A 837 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.8153 (t80) REVERT: A 868 LYS cc_start: 0.8240 (mtpp) cc_final: 0.8015 (mtpp) REVERT: A 886 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7882 (tt0) REVERT: A 911 GLU cc_start: 0.8003 (tt0) cc_final: 0.7758 (mt-10) REVERT: A 926 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 981 HIS cc_start: 0.7991 (m90) cc_final: 0.7775 (m-70) REVERT: A 1044 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 1066 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: A 1075 ILE cc_start: 0.8348 (mm) cc_final: 0.8135 (mm) REVERT: A 1110 GLN cc_start: 0.7680 (mp10) cc_final: 0.7244 (mp-120) REVERT: A 1115 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 1122 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1139 ASP cc_start: 0.7559 (m-30) cc_final: 0.7286 (m-30) REVERT: A 1144 ASP cc_start: 0.7199 (p0) cc_final: 0.6996 (p0) REVERT: A 1190 ARG cc_start: 0.7334 (tpt170) cc_final: 0.7020 (mmt180) outliers start: 29 outliers final: 18 residues processed: 274 average time/residue: 0.1135 time to fit residues: 41.2332 Evaluate side-chains 271 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 321 VAL Chi-restraints excluded: chain A residue 371 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN 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 = 0.137597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119144 restraints weight = 12595.456| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.02 r_work: 0.3382 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8395 Z= 0.140 Angle : 0.574 13.265 11384 Z= 0.291 Chirality : 0.039 0.166 1368 Planarity : 0.004 0.035 1404 Dihedral : 6.045 57.146 1132 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.12 % Allowed : 19.15 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.27), residues: 1032 helix: 1.44 (0.19), residues: 759 sheet: 0.43 (0.85), residues: 38 loop : -1.34 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 733 TYR 0.008 0.001 TYR A 309 PHE 0.027 0.001 PHE A 766 TRP 0.011 0.001 TRP A 353 HIS 0.002 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8395) covalent geometry : angle 0.57361 (11384) hydrogen bonds : bond 0.04651 ( 618) hydrogen bonds : angle 4.18636 ( 1833) *********************** 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 293 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8247 (p) cc_final: 0.7950 (m) REVERT: A 120 VAL cc_start: 0.7678 (t) cc_final: 0.7365 (m) REVERT: A 149 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 154 MET cc_start: 0.8504 (tpp) cc_final: 0.7641 (tpp) REVERT: A 155 ASP cc_start: 0.7966 (t0) cc_final: 0.7616 (t0) REVERT: A 176 VAL cc_start: 0.8486 (p) cc_final: 0.8213 (t) REVERT: A 190 ASN cc_start: 0.8225 (p0) cc_final: 0.8000 (p0) REVERT: A 197 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 231 GLU cc_start: 0.7467 (tt0) cc_final: 0.7246 (tt0) REVERT: A 233 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 246 ASN cc_start: 0.8274 (m-40) cc_final: 0.7924 (m110) REVERT: A 277 LEU cc_start: 0.8545 (mm) cc_final: 0.8288 (mp) REVERT: A 321 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7778 (m) REVERT: A 338 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8361 (mtmm) REVERT: A 375 LYS cc_start: 0.8310 (ttpt) cc_final: 0.8090 (ttmm) REVERT: A 377 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 386 PHE cc_start: 0.8038 (t80) cc_final: 0.7566 (t80) REVERT: A 491 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8306 (ttm-80) REVERT: A 516 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8013 (ttt90) REVERT: A 524 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: A 573 ARG cc_start: 0.7318 (mmm160) cc_final: 0.6665 (mmm160) REVERT: A 588 LYS cc_start: 0.8154 (tppt) cc_final: 0.7882 (tppt) REVERT: A 598 PHE cc_start: 0.8735 (t80) cc_final: 0.8355 (t80) REVERT: A 609 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: A 616 GLU cc_start: 0.7550 (pt0) cc_final: 0.7270 (pt0) REVERT: A 621 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: A 633 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8418 (mmtt) REVERT: A 637 ILE cc_start: 0.8450 (tp) cc_final: 0.8160 (tp) REVERT: A 644 LEU cc_start: 0.8492 (mt) cc_final: 0.8290 (mp) REVERT: A 678 MET cc_start: 0.6530 (ppp) cc_final: 0.6164 (ppp) REVERT: A 685 ASN cc_start: 0.8623 (m-40) cc_final: 0.8173 (m-40) REVERT: A 697 MET cc_start: 0.6811 (mmm) cc_final: 0.6390 (mmm) REVERT: A 824 VAL cc_start: 0.8641 (t) cc_final: 0.8289 (m) REVERT: A 831 ASN cc_start: 0.8031 (m-40) cc_final: 0.7801 (m110) REVERT: A 837 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8117 (t80) REVERT: A 868 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7950 (mtpp) REVERT: A 886 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7958 (tt0) REVERT: A 926 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 981 HIS cc_start: 0.7984 (m90) cc_final: 0.7776 (m-70) REVERT: A 994 GLU cc_start: 0.8173 (pm20) cc_final: 0.7703 (pm20) REVERT: A 1044 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 1066 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: A 1075 ILE cc_start: 0.8312 (mm) cc_final: 0.8107 (mm) REVERT: A 1110 GLN cc_start: 0.7721 (mp10) cc_final: 0.7276 (mp-120) REVERT: A 1115 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: A 1122 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 1144 ASP cc_start: 0.7213 (p0) cc_final: 0.6994 (p0) REVERT: A 1174 LEU cc_start: 0.7495 (mt) cc_final: 0.7284 (mp) REVERT: A 1190 ARG cc_start: 0.7323 (tpt170) cc_final: 0.7014 (mmt180) outliers start: 37 outliers final: 20 residues processed: 278 average time/residue: 0.1136 time to fit residues: 41.5110 Evaluate side-chains 274 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 987 VAL Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1068 ILE 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 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 9 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 30 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 165 GLN A 764 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118905 restraints weight = 12495.556| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.98 r_work: 0.3382 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2949 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= 0.151 Angle : 0.574 13.799 11384 Z= 0.292 Chirality : 0.040 0.181 1368 Planarity : 0.004 0.034 1404 Dihedral : 6.034 59.270 1132 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.23 % Allowed : 20.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.27), residues: 1032 helix: 1.50 (0.19), residues: 761 sheet: 0.51 (0.83), residues: 38 loop : -1.24 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1162 TYR 0.009 0.001 TYR A 309 PHE 0.028 0.001 PHE A 766 TRP 0.010 0.001 TRP A 353 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8395) covalent geometry : angle 0.57360 (11384) hydrogen bonds : bond 0.04712 ( 618) hydrogen bonds : angle 4.18897 ( 1833) *********************** 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 293 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8236 (p) cc_final: 0.7942 (m) REVERT: A 120 VAL cc_start: 0.7726 (t) cc_final: 0.7398 (m) REVERT: A 149 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 154 MET cc_start: 0.8499 (tpp) cc_final: 0.7659 (tpp) REVERT: A 155 ASP cc_start: 0.7979 (t0) cc_final: 0.7638 (t0) REVERT: A 176 VAL cc_start: 0.8497 (p) cc_final: 0.8245 (t) REVERT: A 190 ASN cc_start: 0.8225 (p0) cc_final: 0.7980 (p0) REVERT: A 197 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7877 (mt-10) REVERT: A 206 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8172 (t) REVERT: A 231 GLU cc_start: 0.7490 (tt0) cc_final: 0.7263 (tt0) REVERT: A 233 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7572 (tm-30) REVERT: A 246 ASN cc_start: 0.8258 (m-40) cc_final: 0.7923 (m110) REVERT: A 277 LEU cc_start: 0.8539 (mm) cc_final: 0.8299 (mp) REVERT: A 321 VAL cc_start: 0.8023 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 338 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8386 (mtmm) REVERT: A 377 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8296 (mp) REVERT: A 386 PHE cc_start: 0.8004 (t80) cc_final: 0.7528 (t80) REVERT: A 412 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6999 (mtm180) REVERT: A 465 LEU cc_start: 0.8451 (mt) cc_final: 0.8207 (mp) REVERT: A 477 LEU cc_start: 0.8523 (tp) cc_final: 0.8290 (tp) REVERT: A 491 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8305 (ttm-80) REVERT: A 499 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7784 (ttp80) REVERT: A 516 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8027 (ttt90) REVERT: A 524 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7598 (m-30) REVERT: A 573 ARG cc_start: 0.7339 (mmm160) cc_final: 0.6615 (mmm160) REVERT: A 588 LYS cc_start: 0.8108 (tppt) cc_final: 0.7844 (tppt) REVERT: A 598 PHE cc_start: 0.8711 (t80) cc_final: 0.8170 (t80) REVERT: A 609 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7416 (mmm-85) REVERT: A 616 GLU cc_start: 0.7564 (pt0) cc_final: 0.7285 (pt0) REVERT: A 621 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: A 633 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8382 (mmtt) REVERT: A 637 ILE cc_start: 0.8477 (tp) cc_final: 0.8206 (tp) REVERT: A 644 LEU cc_start: 0.8464 (mt) cc_final: 0.8260 (mp) REVERT: A 678 MET cc_start: 0.6529 (ppp) cc_final: 0.6145 (ppp) REVERT: A 685 ASN cc_start: 0.8545 (m-40) cc_final: 0.8122 (m-40) REVERT: A 756 ARG cc_start: 0.7658 (mmp80) cc_final: 0.6276 (pmt170) REVERT: A 824 VAL cc_start: 0.8629 (t) cc_final: 0.8272 (m) REVERT: A 831 ASN cc_start: 0.8049 (m-40) cc_final: 0.7799 (m110) REVERT: A 835 LEU cc_start: 0.8766 (tp) cc_final: 0.8494 (tt) REVERT: A 837 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 868 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7940 (mtpp) REVERT: A 876 LEU cc_start: 0.8479 (mt) cc_final: 0.8135 (mp) REVERT: A 886 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7983 (tt0) REVERT: A 900 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7986 (mm110) REVERT: A 911 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7655 (mt-10) REVERT: A 926 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 940 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7819 (mtt90) REVERT: A 981 HIS cc_start: 0.7955 (m90) cc_final: 0.7753 (m-70) REVERT: A 994 GLU cc_start: 0.8208 (pm20) cc_final: 0.7762 (pm20) REVERT: A 1044 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 1066 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: A 1110 GLN cc_start: 0.7745 (mp10) cc_final: 0.7293 (mp-120) REVERT: A 1115 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: A 1122 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 1144 ASP cc_start: 0.7217 (p0) cc_final: 0.6981 (p0) REVERT: A 1174 LEU cc_start: 0.7510 (mt) cc_final: 0.7288 (mp) REVERT: A 1190 ARG cc_start: 0.7311 (tpt170) cc_final: 0.7010 (mmt180) outliers start: 38 outliers final: 19 residues processed: 275 average time/residue: 0.1155 time to fit residues: 41.8283 Evaluate side-chains 285 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 344 GLU 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 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 987 VAL Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1068 ILE 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 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 292 HIS ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118737 restraints weight = 12391.341| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.96 r_work: 0.3374 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8395 Z= 0.169 Angle : 0.589 14.063 11384 Z= 0.301 Chirality : 0.040 0.168 1368 Planarity : 0.004 0.034 1404 Dihedral : 6.043 56.725 1132 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.45 % Allowed : 22.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.27), residues: 1032 helix: 1.51 (0.19), residues: 760 sheet: 0.59 (0.82), residues: 38 loop : -1.24 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1162 TYR 0.010 0.001 TYR A 309 PHE 0.024 0.001 PHE A 766 TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8395) covalent geometry : angle 0.58883 (11384) hydrogen bonds : bond 0.04860 ( 618) hydrogen bonds : angle 4.20011 ( 1833) *********************** 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 284 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8247 (p) cc_final: 0.7944 (m) REVERT: A 120 VAL cc_start: 0.7763 (t) cc_final: 0.7447 (m) REVERT: A 149 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 154 MET cc_start: 0.8482 (tpp) cc_final: 0.7653 (tpp) REVERT: A 155 ASP cc_start: 0.8002 (t0) cc_final: 0.7624 (t0) REVERT: A 176 VAL cc_start: 0.8524 (p) cc_final: 0.8273 (t) REVERT: A 190 ASN cc_start: 0.8264 (p0) cc_final: 0.8039 (p0) REVERT: A 197 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7901 (mt-10) REVERT: A 206 SER cc_start: 0.8562 (m) cc_final: 0.8140 (t) REVERT: A 231 GLU cc_start: 0.7533 (tt0) cc_final: 0.7285 (tt0) REVERT: A 233 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7589 (tm-30) REVERT: A 277 LEU cc_start: 0.8561 (mm) cc_final: 0.8312 (mp) REVERT: A 321 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (m) REVERT: A 338 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8381 (mtmm) REVERT: A 386 PHE cc_start: 0.8010 (t80) cc_final: 0.7561 (t80) REVERT: A 387 TYR cc_start: 0.8320 (m-10) cc_final: 0.8108 (m-10) REVERT: A 465 LEU cc_start: 0.8449 (mt) cc_final: 0.8207 (mp) REVERT: A 477 LEU cc_start: 0.8557 (tp) cc_final: 0.8288 (tp) REVERT: A 491 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8300 (ttm-80) REVERT: A 499 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7762 (ttp80) REVERT: A 516 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8029 (ttt90) REVERT: A 524 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: A 573 ARG cc_start: 0.7359 (mmm160) cc_final: 0.6619 (mmm160) REVERT: A 588 LYS cc_start: 0.8122 (tppt) cc_final: 0.7850 (tppt) REVERT: A 598 PHE cc_start: 0.8711 (t80) cc_final: 0.8184 (t80) REVERT: A 609 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7396 (mmm-85) REVERT: A 616 GLU cc_start: 0.7581 (pt0) cc_final: 0.7296 (pt0) REVERT: A 621 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 633 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8406 (mmtt) REVERT: A 637 ILE cc_start: 0.8580 (tp) cc_final: 0.8311 (tp) REVERT: A 644 LEU cc_start: 0.8491 (mt) cc_final: 0.8279 (mp) REVERT: A 651 LEU cc_start: 0.8797 (tt) cc_final: 0.8391 (tp) REVERT: A 678 MET cc_start: 0.6577 (ppp) cc_final: 0.6189 (ppp) REVERT: A 685 ASN cc_start: 0.8546 (m-40) cc_final: 0.8144 (m-40) REVERT: A 756 ARG cc_start: 0.7635 (mmp80) cc_final: 0.6330 (pmt170) REVERT: A 773 VAL cc_start: 0.8268 (t) cc_final: 0.8053 (p) REVERT: A 824 VAL cc_start: 0.8627 (t) cc_final: 0.8264 (m) REVERT: A 831 ASN cc_start: 0.8076 (m-40) cc_final: 0.7819 (m110) REVERT: A 835 LEU cc_start: 0.8702 (tp) cc_final: 0.8483 (tt) REVERT: A 837 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 868 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7938 (mtpp) REVERT: A 876 LEU cc_start: 0.8456 (mt) cc_final: 0.8113 (mp) REVERT: A 886 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8010 (tt0) REVERT: A 911 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 926 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 940 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7833 (mtt90) REVERT: A 994 GLU cc_start: 0.8205 (pm20) cc_final: 0.7780 (pm20) REVERT: A 999 PHE cc_start: 0.7661 (m-10) cc_final: 0.7451 (m-10) REVERT: A 1044 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 1066 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: A 1105 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 1110 GLN cc_start: 0.7808 (mp10) cc_final: 0.7336 (mp-120) REVERT: A 1115 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: A 1122 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 1144 ASP cc_start: 0.7230 (p0) cc_final: 0.7004 (p0) REVERT: A 1174 LEU cc_start: 0.7568 (mt) cc_final: 0.7321 (mp) REVERT: A 1190 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6994 (mmt180) outliers start: 31 outliers final: 19 residues processed: 271 average time/residue: 0.1127 time to fit residues: 40.1661 Evaluate side-chains 281 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL 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 321 VAL Chi-restraints excluded: chain A residue 344 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 0.0040 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 691 ASN ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119767 restraints weight = 12525.986| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.99 r_work: 0.3390 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3218 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= 0.140 Angle : 0.581 13.695 11384 Z= 0.297 Chirality : 0.040 0.177 1368 Planarity : 0.004 0.033 1404 Dihedral : 5.723 56.921 1130 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.27), residues: 1032 helix: 1.62 (0.19), residues: 761 sheet: 0.70 (0.82), residues: 38 loop : -1.21 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1162 TYR 0.008 0.001 TYR A 309 PHE 0.025 0.001 PHE A 766 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8395) covalent geometry : angle 0.58059 (11384) hydrogen bonds : bond 0.04600 ( 618) hydrogen bonds : angle 4.13900 ( 1833) *********************** 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: 37 poor density : 252 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8184 (p) cc_final: 0.7873 (m) REVERT: A 120 VAL cc_start: 0.7745 (t) cc_final: 0.7441 (m) REVERT: A 149 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 154 MET cc_start: 0.8476 (tpp) cc_final: 0.7642 (tpp) REVERT: A 155 ASP cc_start: 0.8015 (t0) cc_final: 0.7649 (t0) REVERT: A 176 VAL cc_start: 0.8502 (p) cc_final: 0.8236 (t) REVERT: A 190 ASN cc_start: 0.8227 (p0) cc_final: 0.8003 (p0) REVERT: A 206 SER cc_start: 0.8580 (m) cc_final: 0.8150 (t) REVERT: A 217 LEU cc_start: 0.8659 (mt) cc_final: 0.8255 (mp) REVERT: A 231 GLU cc_start: 0.7535 (tt0) cc_final: 0.7277 (tt0) REVERT: A 233 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 246 ASN cc_start: 0.8259 (m-40) cc_final: 0.7919 (m110) REVERT: A 277 LEU cc_start: 0.8540 (mm) cc_final: 0.8300 (mp) REVERT: A 286 THR cc_start: 0.8615 (m) cc_final: 0.8350 (p) REVERT: A 321 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7818 (m) REVERT: A 386 PHE cc_start: 0.7966 (t80) cc_final: 0.7498 (t80) REVERT: A 387 TYR cc_start: 0.8314 (m-10) cc_final: 0.8073 (m-10) REVERT: A 412 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6970 (mtm180) REVERT: A 465 LEU cc_start: 0.8428 (mt) cc_final: 0.8183 (mp) REVERT: A 477 LEU cc_start: 0.8523 (tp) cc_final: 0.8261 (tp) REVERT: A 491 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8275 (ttm-80) REVERT: A 499 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7762 (ttp80) REVERT: A 516 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8017 (ttt90) REVERT: A 524 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7596 (m-30) REVERT: A 573 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6604 (mmm160) REVERT: A 588 LYS cc_start: 0.8080 (tppt) cc_final: 0.7798 (tppt) REVERT: A 598 PHE cc_start: 0.8696 (t80) cc_final: 0.8208 (t80) REVERT: A 609 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7405 (mmm-85) REVERT: A 616 GLU cc_start: 0.7552 (pt0) cc_final: 0.7270 (pt0) REVERT: A 621 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: A 633 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8357 (mmtt) REVERT: A 637 ILE cc_start: 0.8513 (tp) cc_final: 0.8246 (tp) REVERT: A 678 MET cc_start: 0.6601 (ppp) cc_final: 0.6209 (ppp) REVERT: A 685 ASN cc_start: 0.8534 (m-40) cc_final: 0.8142 (m-40) REVERT: A 773 VAL cc_start: 0.8219 (t) cc_final: 0.7989 (p) REVERT: A 824 VAL cc_start: 0.8625 (t) cc_final: 0.8266 (m) REVERT: A 831 ASN cc_start: 0.8022 (m-40) cc_final: 0.7756 (m110) REVERT: A 835 LEU cc_start: 0.8690 (tp) cc_final: 0.8474 (tt) REVERT: A 837 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 868 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7932 (mtpp) REVERT: A 876 LEU cc_start: 0.8458 (mt) cc_final: 0.8103 (mp) REVERT: A 911 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 926 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 987 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 994 GLU cc_start: 0.8223 (pm20) cc_final: 0.7992 (pm20) REVERT: A 1044 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 1066 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 1105 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 1110 GLN cc_start: 0.7808 (mp10) cc_final: 0.7339 (mp-120) REVERT: A 1122 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7538 (mm-30) REVERT: A 1144 ASP cc_start: 0.7272 (p0) cc_final: 0.7058 (p0) REVERT: A 1174 LEU cc_start: 0.7480 (mt) cc_final: 0.7270 (mp) REVERT: A 1190 ARG cc_start: 0.7278 (tpt170) cc_final: 0.6987 (mmt180) outliers start: 37 outliers final: 25 residues processed: 273 average time/residue: 0.1092 time to fit residues: 39.6904 Evaluate side-chains 277 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 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 321 VAL 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 451 ILE 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 805 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 888 GLU 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 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 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 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 A 981 HIS A1074 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119653 restraints weight = 12469.694| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.99 r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3306 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= 0.145 Angle : 0.587 13.806 11384 Z= 0.300 Chirality : 0.040 0.180 1368 Planarity : 0.004 0.032 1404 Dihedral : 5.717 57.693 1130 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.45 % Allowed : 22.61 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.27), residues: 1032 helix: 1.63 (0.19), residues: 762 sheet: 0.77 (0.82), residues: 38 loop : -1.16 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1162 TYR 0.008 0.001 TYR A 309 PHE 0.026 0.001 PHE A 766 TRP 0.014 0.001 TRP A 643 HIS 0.003 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8395) covalent geometry : angle 0.58735 (11384) hydrogen bonds : bond 0.04613 ( 618) hydrogen bonds : angle 4.12780 ( 1833) *********************** 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 282 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8178 (p) cc_final: 0.7875 (m) REVERT: A 120 VAL cc_start: 0.7722 (t) cc_final: 0.7428 (m) REVERT: A 149 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 154 MET cc_start: 0.8469 (tpp) cc_final: 0.7602 (tpp) REVERT: A 155 ASP cc_start: 0.8009 (t0) cc_final: 0.7659 (t0) REVERT: A 176 VAL cc_start: 0.8506 (p) cc_final: 0.8254 (t) REVERT: A 190 ASN cc_start: 0.8221 (p0) cc_final: 0.8002 (p0) REVERT: A 206 SER cc_start: 0.8574 (m) cc_final: 0.8139 (t) REVERT: A 217 LEU cc_start: 0.8672 (mt) cc_final: 0.8268 (mp) REVERT: A 231 GLU cc_start: 0.7529 (tt0) cc_final: 0.7273 (tt0) REVERT: A 233 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 246 ASN cc_start: 0.8256 (m-40) cc_final: 0.7926 (m110) REVERT: A 277 LEU cc_start: 0.8545 (mm) cc_final: 0.8302 (mp) REVERT: A 286 THR cc_start: 0.8608 (m) cc_final: 0.8339 (p) REVERT: A 321 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7825 (m) REVERT: A 386 PHE cc_start: 0.7955 (t80) cc_final: 0.7495 (t80) REVERT: A 387 TYR cc_start: 0.8306 (m-10) cc_final: 0.8090 (m-10) REVERT: A 412 ARG cc_start: 0.7294 (mtm180) cc_final: 0.7000 (mtm180) REVERT: A 465 LEU cc_start: 0.8423 (mt) cc_final: 0.8171 (mp) REVERT: A 477 LEU cc_start: 0.8501 (tp) cc_final: 0.8212 (tp) REVERT: A 491 ARG cc_start: 0.8524 (tpp80) cc_final: 0.8273 (ttm-80) REVERT: A 516 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8030 (ttt90) REVERT: A 524 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7597 (m-30) REVERT: A 573 ARG cc_start: 0.7355 (mmm160) cc_final: 0.6579 (mmm160) REVERT: A 588 LYS cc_start: 0.8050 (tppt) cc_final: 0.7786 (tppt) REVERT: A 598 PHE cc_start: 0.8706 (t80) cc_final: 0.8194 (t80) REVERT: A 609 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7430 (mmm-85) REVERT: A 616 GLU cc_start: 0.7525 (pt0) cc_final: 0.7236 (pt0) REVERT: A 621 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: A 633 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8377 (mmtt) REVERT: A 637 ILE cc_start: 0.8484 (tp) cc_final: 0.8249 (tp) REVERT: A 678 MET cc_start: 0.6605 (ppp) cc_final: 0.6207 (ppp) REVERT: A 685 ASN cc_start: 0.8519 (m-40) cc_final: 0.8126 (m-40) REVERT: A 756 ARG cc_start: 0.7480 (mmp80) cc_final: 0.6296 (ppt170) REVERT: A 773 VAL cc_start: 0.8280 (t) cc_final: 0.8064 (p) REVERT: A 824 VAL cc_start: 0.8631 (t) cc_final: 0.8269 (m) REVERT: A 831 ASN cc_start: 0.8018 (m-40) cc_final: 0.7754 (m110) REVERT: A 835 LEU cc_start: 0.8692 (tp) cc_final: 0.8465 (tt) REVERT: A 837 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8080 (t80) REVERT: A 847 GLU cc_start: 0.8068 (tp30) cc_final: 0.7830 (tp30) REVERT: A 876 LEU cc_start: 0.8451 (mt) cc_final: 0.8102 (mp) REVERT: A 911 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 926 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 994 GLU cc_start: 0.8228 (pm20) cc_final: 0.7989 (pm20) REVERT: A 1044 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 1066 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7730 (m-80) REVERT: A 1105 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 1110 GLN cc_start: 0.7864 (mp10) cc_final: 0.7411 (mp-120) REVERT: A 1122 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 1174 LEU cc_start: 0.7450 (mt) cc_final: 0.7234 (mp) REVERT: A 1190 ARG cc_start: 0.7272 (tpt170) cc_final: 0.7036 (mmt180) outliers start: 31 outliers final: 23 residues processed: 271 average time/residue: 0.1069 time to fit residues: 38.7398 Evaluate side-chains 274 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 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 321 VAL 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 888 GLU 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 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 55 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118688 restraints weight = 12422.768| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.97 r_work: 0.3378 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3446 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= 0.176 Angle : 0.625 14.306 11384 Z= 0.320 Chirality : 0.041 0.183 1368 Planarity : 0.004 0.032 1404 Dihedral : 5.821 58.494 1130 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.45 % Allowed : 22.94 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1032 helix: 1.56 (0.19), residues: 763 sheet: 0.82 (0.82), residues: 38 loop : -1.17 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1162 TYR 0.011 0.001 TYR A 309 PHE 0.027 0.002 PHE A 766 TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8395) covalent geometry : angle 0.62451 (11384) hydrogen bonds : bond 0.04954 ( 618) hydrogen bonds : angle 4.24456 ( 1833) *********************** 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 279 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8231 (p) cc_final: 0.7921 (m) REVERT: A 120 VAL cc_start: 0.7739 (t) cc_final: 0.7442 (m) REVERT: A 149 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 154 MET cc_start: 0.8500 (tpp) cc_final: 0.7679 (tpp) REVERT: A 155 ASP cc_start: 0.8004 (t0) cc_final: 0.7627 (t0) REVERT: A 176 VAL cc_start: 0.8537 (p) cc_final: 0.8295 (t) REVERT: A 190 ASN cc_start: 0.8238 (p0) cc_final: 0.8016 (p0) REVERT: A 205 MET cc_start: 0.8132 (mmt) cc_final: 0.7908 (mmp) REVERT: A 206 SER cc_start: 0.8577 (m) cc_final: 0.8161 (t) REVERT: A 217 LEU cc_start: 0.8674 (mt) cc_final: 0.8273 (mp) REVERT: A 231 GLU cc_start: 0.7539 (tt0) cc_final: 0.7296 (tt0) REVERT: A 233 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7523 (tm-30) REVERT: A 277 LEU cc_start: 0.8569 (mm) cc_final: 0.8319 (mp) REVERT: A 321 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7867 (m) REVERT: A 386 PHE cc_start: 0.7975 (t80) cc_final: 0.7510 (t80) REVERT: A 387 TYR cc_start: 0.8336 (m-10) cc_final: 0.8135 (m-10) REVERT: A 412 ARG cc_start: 0.7293 (mtm180) cc_final: 0.6991 (mtm180) REVERT: A 465 LEU cc_start: 0.8439 (mt) cc_final: 0.8189 (mp) REVERT: A 477 LEU cc_start: 0.8565 (tp) cc_final: 0.8309 (tp) REVERT: A 491 ARG cc_start: 0.8544 (tpp80) cc_final: 0.8276 (ttm-80) REVERT: A 516 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.8000 (ttt90) REVERT: A 524 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: A 573 ARG cc_start: 0.7379 (mmm160) cc_final: 0.6592 (mmm160) REVERT: A 588 LYS cc_start: 0.8069 (tppt) cc_final: 0.7807 (tppt) REVERT: A 598 PHE cc_start: 0.8690 (t80) cc_final: 0.8194 (t80) REVERT: A 609 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7402 (mmm-85) REVERT: A 616 GLU cc_start: 0.7555 (pt0) cc_final: 0.7264 (pt0) REVERT: A 621 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 633 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8365 (mmtt) REVERT: A 678 MET cc_start: 0.6639 (ppp) cc_final: 0.6242 (ppp) REVERT: A 685 ASN cc_start: 0.8496 (m-40) cc_final: 0.8208 (m-40) REVERT: A 756 ARG cc_start: 0.7336 (mmp80) cc_final: 0.6350 (ppt170) REVERT: A 773 VAL cc_start: 0.8251 (t) cc_final: 0.8047 (p) REVERT: A 824 VAL cc_start: 0.8613 (t) cc_final: 0.8254 (m) REVERT: A 831 ASN cc_start: 0.8077 (m-40) cc_final: 0.7807 (m110) REVERT: A 837 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8011 (t80) REVERT: A 876 LEU cc_start: 0.8430 (mt) cc_final: 0.8097 (mp) REVERT: A 911 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 926 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 994 GLU cc_start: 0.8225 (pm20) cc_final: 0.7822 (pm20) REVERT: A 1044 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 1066 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: A 1105 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7708 (tm-30) REVERT: A 1110 GLN cc_start: 0.7901 (mp10) cc_final: 0.7428 (mp-120) REVERT: A 1122 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 1174 LEU cc_start: 0.7380 (mt) cc_final: 0.7128 (mp) REVERT: A 1190 ARG cc_start: 0.7348 (tpt170) cc_final: 0.7076 (mmt180) outliers start: 31 outliers final: 24 residues processed: 268 average time/residue: 0.1107 time to fit residues: 39.6066 Evaluate side-chains 274 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 269 LEU Chi-restraints excluded: chain A residue 321 VAL 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 767 ASP 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 863 ILE 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 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 65 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119340 restraints weight = 12402.877| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.97 r_work: 0.3386 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3504 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= 0.161 Angle : 0.621 14.139 11384 Z= 0.317 Chirality : 0.041 0.191 1368 Planarity : 0.004 0.032 1404 Dihedral : 5.654 59.029 1128 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.23 % Allowed : 23.61 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1032 helix: 1.58 (0.19), residues: 763 sheet: 0.39 (0.72), residues: 48 loop : -1.21 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1162 TYR 0.009 0.001 TYR A 309 PHE 0.028 0.001 PHE A 766 TRP 0.012 0.001 TRP A 643 HIS 0.003 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8395) covalent geometry : angle 0.62094 (11384) hydrogen bonds : bond 0.04793 ( 618) hydrogen bonds : angle 4.21895 ( 1833) ********************** 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 272 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 VAL cc_start: 0.8197 (p) cc_final: 0.7897 (m) REVERT: A 120 VAL cc_start: 0.7767 (t) cc_final: 0.7486 (m) REVERT: A 149 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7337 (tm-30) REVERT: A 154 MET cc_start: 0.8497 (tpp) cc_final: 0.7697 (tpp) REVERT: A 155 ASP cc_start: 0.7987 (t0) cc_final: 0.7644 (t0) REVERT: A 176 VAL cc_start: 0.8527 (p) cc_final: 0.8277 (t) REVERT: A 190 ASN cc_start: 0.8224 (p0) cc_final: 0.8014 (p0) REVERT: A 206 SER cc_start: 0.8577 (m) cc_final: 0.8345 (t) REVERT: A 217 LEU cc_start: 0.8610 (mt) cc_final: 0.8210 (mp) REVERT: A 231 GLU cc_start: 0.7538 (tt0) cc_final: 0.7283 (tt0) REVERT: A 233 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 277 LEU cc_start: 0.8566 (mm) cc_final: 0.8315 (mp) REVERT: A 303 ILE cc_start: 0.8585 (mp) cc_final: 0.8280 (mp) REVERT: A 321 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (m) REVERT: A 386 PHE cc_start: 0.7949 (t80) cc_final: 0.7508 (t80) REVERT: A 412 ARG cc_start: 0.7318 (mtm180) cc_final: 0.7024 (mtm180) REVERT: A 477 LEU cc_start: 0.8532 (tp) cc_final: 0.8263 (tp) REVERT: A 491 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8248 (ttm-80) REVERT: A 516 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8036 (ttt90) REVERT: A 524 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: A 573 ARG cc_start: 0.7339 (mmm160) cc_final: 0.6557 (mmm160) REVERT: A 588 LYS cc_start: 0.8028 (tppt) cc_final: 0.7764 (tppt) REVERT: A 598 PHE cc_start: 0.8699 (t80) cc_final: 0.8170 (t80) REVERT: A 609 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7371 (mmm-85) REVERT: A 616 GLU cc_start: 0.7526 (pt0) cc_final: 0.7234 (pt0) REVERT: A 621 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: A 633 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8349 (mmtt) REVERT: A 678 MET cc_start: 0.6618 (ppp) cc_final: 0.6231 (ppp) REVERT: A 685 ASN cc_start: 0.8442 (m-40) cc_final: 0.8156 (m-40) REVERT: A 698 GLU cc_start: 0.7850 (pp20) cc_final: 0.7607 (tm-30) REVERT: A 756 ARG cc_start: 0.7381 (mmp80) cc_final: 0.6416 (ptt-90) REVERT: A 824 VAL cc_start: 0.8613 (t) cc_final: 0.8252 (m) REVERT: A 831 ASN cc_start: 0.8031 (m-40) cc_final: 0.7759 (m110) REVERT: A 832 GLN cc_start: 0.8105 (tt0) cc_final: 0.7785 (tp-100) REVERT: A 837 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 876 LEU cc_start: 0.8435 (mt) cc_final: 0.8076 (mp) REVERT: A 881 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7940 (mt-10) REVERT: A 911 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7624 (mt-10) REVERT: A 926 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 994 GLU cc_start: 0.8197 (pm20) cc_final: 0.7962 (pm20) REVERT: A 1044 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 1066 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: A 1104 MET cc_start: 0.8334 (ttt) cc_final: 0.7993 (mtt) REVERT: A 1105 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 1110 GLN cc_start: 0.7879 (mp10) cc_final: 0.7390 (mp-120) REVERT: A 1122 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 1174 LEU cc_start: 0.7385 (mt) cc_final: 0.7142 (mp) REVERT: A 1190 ARG cc_start: 0.7313 (tpt170) cc_final: 0.7044 (mmt180) outliers start: 29 outliers final: 22 residues processed: 263 average time/residue: 0.1098 time to fit residues: 38.3930 Evaluate side-chains 266 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 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 321 VAL 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 805 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 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 30 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN A 981 HIS A1120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118701 restraints weight = 12480.349| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.98 r_work: 0.3379 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3621 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= 0.176 Angle : 0.644 14.604 11384 Z= 0.324 Chirality : 0.041 0.187 1368 Planarity : 0.004 0.036 1404 Dihedral : 5.633 59.802 1128 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 23.94 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.26), residues: 1032 helix: 1.51 (0.19), residues: 769 sheet: 0.30 (0.71), residues: 48 loop : -1.25 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1162 TYR 0.017 0.001 TYR A 387 PHE 0.028 0.001 PHE A 766 TRP 0.010 0.001 TRP A 643 HIS 0.004 0.000 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8395) covalent geometry : angle 0.64365 (11384) hydrogen bonds : bond 0.04958 ( 618) hydrogen bonds : angle 4.26482 ( 1833) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.51 seconds wall clock time: 43 minutes 3.46 seconds (2583.46 seconds total)