Starting phenix.real_space_refine on Fri Aug 22 19:41:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efe_28081/08_2025/8efe_28081.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4534 2.51 5 N 1215 2.21 5 O 1343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 7135 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5967 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 28, 'TRANS': 711} Chain breaks: 3 Chain: "B" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1140 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.77, per 1000 atoms: 0.25 Number of scatterers: 7135 At special positions: 0 Unit cell: (139.062, 88.396, 104.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 2 15.00 Mg 1 11.99 O 1343 8.00 N 1215 7.00 C 4534 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: 0.56 Conformation dependent library (CDL) restraints added in 371.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 57.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.607A pdb=" N ASP A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.940A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 removed outlier: 4.356A pdb=" N TYR A 134 " --> pdb=" O LEU A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 169 removed outlier: 3.725A pdb=" N ILE A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 217 through 231 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.818A pdb=" N VAL A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 removed outlier: 3.971A pdb=" N TYR A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.667A pdb=" N LEU A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.707A pdb=" N GLN A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.843A pdb=" N LYS A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 401 Processing helix chain 'A' and resid 416 through 448 Processing helix chain 'A' and resid 472 through 505 Processing helix chain 'A' and resid 517 through 526 removed outlier: 4.078A pdb=" N ILE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 removed outlier: 3.568A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 Processing helix chain 'A' and resid 592 through 598 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 647 through 664 removed outlier: 4.087A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 697 through 708 removed outlier: 4.146A pdb=" N GLY A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 766 through 796 Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.827A pdb=" N LEU B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 104 through 115 Proline residue: B 109 - end of helix Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.773A pdb=" N VAL B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.712A pdb=" N VAL B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.769A pdb=" N VAL B 188 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.388A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.831A pdb=" N SER A 118 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 122 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN A 172 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 460 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 174 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 462 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 176 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE A 456 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE A 250 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY A 458 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 248 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU A 460 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 246 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 406 Processing sheet with id=AA6, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.031A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.721A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142 355 hydrogen bonds defined for protein. 1041 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: 0.99 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2328 1.34 - 1.46: 947 1.46 - 1.57: 3926 1.57 - 1.69: 3 1.69 - 1.81: 70 Bond restraints: 7274 Sorted by residual: bond pdb=" C LYS A 365 " pdb=" O LYS A 365 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.26e-02 6.30e+03 2.01e+00 bond pdb=" CA LYS A 365 " pdb=" C LYS A 365 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.34e-02 5.57e+03 1.69e+00 bond pdb=" CA GLN A 372 " pdb=" C GLN A 372 " ideal model delta sigma weight residual 1.525 1.509 0.016 1.28e-02 6.10e+03 1.47e+00 bond pdb=" C4 ADP A2002 " pdb=" C5 ADP A2002 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.28e-02 6.10e+03 1.30e+00 ... (remaining 7269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 9553 1.34 - 2.68: 189 2.68 - 4.02: 42 4.02 - 5.36: 11 5.36 - 6.70: 4 Bond angle restraints: 9799 Sorted by residual: angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" O PRO A 375 " ideal model delta sigma weight residual 122.12 118.67 3.45 1.24e+00 6.50e-01 7.75e+00 angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" N ASP A 376 " ideal model delta sigma weight residual 114.65 117.92 -3.27 1.27e+00 6.20e-01 6.61e+00 angle pdb=" O MET A 362 " pdb=" C MET A 362 " pdb=" N LYS A 363 " ideal model delta sigma weight residual 122.96 120.28 2.68 1.13e+00 7.83e-01 5.63e+00 angle pdb=" CB MET A 546 " pdb=" CG MET A 546 " pdb=" SD MET A 546 " ideal model delta sigma weight residual 112.70 119.40 -6.70 3.00e+00 1.11e-01 4.98e+00 angle pdb=" CA MET A 362 " pdb=" C MET A 362 " pdb=" N LYS A 363 " ideal model delta sigma weight residual 115.49 118.16 -2.67 1.24e+00 6.50e-01 4.65e+00 ... (remaining 9794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3917 17.28 - 34.56: 390 34.56 - 51.84: 81 51.84 - 69.13: 17 69.13 - 86.41: 6 Dihedral angle restraints: 4411 sinusoidal: 1840 harmonic: 2571 Sorted by residual: dihedral pdb=" CB GLU A 269 " pdb=" CG GLU A 269 " pdb=" CD GLU A 269 " pdb=" OE1 GLU A 269 " ideal model delta sinusoidal sigma weight residual 0.00 -86.41 86.41 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 90.00 132.97 -42.97 2 1.50e+01 4.44e-03 9.91e+00 dihedral pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " pdb=" CD GLU A 280 " pdb=" OE1 GLU A 280 " ideal model delta sinusoidal sigma weight residual 0.00 -85.37 85.37 1 3.00e+01 1.11e-03 9.81e+00 ... (remaining 4408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.054: 230 0.054 - 0.081: 68 0.081 - 0.108: 42 0.108 - 0.135: 19 Chirality restraints: 1064 Sorted by residual: chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 467 " pdb=" N ILE A 467 " pdb=" C ILE A 467 " pdb=" CB ILE A 467 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 751 " pdb=" N ILE A 751 " pdb=" C ILE A 751 " pdb=" CB ILE A 751 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1061 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 112 " 0.011 2.00e-02 2.50e+03 8.27e-03 1.71e+00 pdb=" CG TRP A 112 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 112 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 112 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 112 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 112 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 112 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.009 2.00e-02 2.50e+03 8.37e-03 1.22e+00 pdb=" CG PHE A 46 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 135 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 136 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.015 5.00e-02 4.00e+02 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 64 2.54 - 3.13: 5892 3.13 - 3.72: 11630 3.72 - 4.31: 15019 4.31 - 4.90: 25044 Nonbonded interactions: 57649 Sorted by model distance: nonbonded pdb=" OG SER A 19 " pdb=" OE1 GLU A 22 " model vdw 1.948 3.040 nonbonded pdb=" O LYS A 189 " pdb=" NE2 GLN A 193 " model vdw 2.054 3.120 nonbonded pdb="MG MG A2001 " pdb=" O3B ADP A2002 " model vdw 2.072 2.170 nonbonded pdb=" OH TYR A 162 " pdb=" O GLY A 256 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR A 185 " pdb="MG MG A2001 " model vdw 2.234 2.170 ... (remaining 57644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.002 0.039 7274 Z= 0.118 Angle : 0.515 6.695 9799 Z= 0.278 Chirality : 0.036 0.135 1064 Planarity : 0.003 0.028 1270 Dihedral : 14.481 86.407 2753 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.52 % Allowed : 0.13 % Favored : 99.35 % 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 (0.30), residues: 876 helix: 2.21 (0.25), residues: 462 sheet: -1.11 (0.63), residues: 75 loop : -0.84 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.013 0.001 TYR A 194 PHE 0.019 0.001 PHE A 46 TRP 0.021 0.002 TRP A 112 HIS 0.002 0.000 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7274) covalent geometry : angle 0.51503 ( 9799) hydrogen bonds : bond 0.12703 ( 355) hydrogen bonds : angle 5.64828 ( 1041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 362 MET cc_start: 0.8874 (mpp) cc_final: 0.8606 (mpp) REVERT: A 465 PHE cc_start: 0.7935 (t80) cc_final: 0.7718 (t80) outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 0.0840 time to fit residues: 7.0407 Evaluate side-chains 50 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS B 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.058696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.038759 restraints weight = 48238.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.039950 restraints weight = 24607.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.040665 restraints weight = 15823.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.041082 restraints weight = 12011.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.041230 restraints weight = 10128.064| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7274 Z= 0.153 Angle : 0.565 5.987 9799 Z= 0.290 Chirality : 0.041 0.149 1064 Planarity : 0.003 0.037 1270 Dihedral : 4.528 36.471 966 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.65 % Allowed : 6.11 % Favored : 93.24 % 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: 0.87 (0.29), residues: 876 helix: 1.91 (0.25), residues: 470 sheet: -0.68 (0.69), residues: 67 loop : -1.09 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.012 0.001 TYR B 123 PHE 0.011 0.001 PHE A 312 TRP 0.008 0.001 TRP A 130 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 7274) covalent geometry : angle 0.56534 ( 9799) hydrogen bonds : bond 0.03362 ( 355) hydrogen bonds : angle 4.69687 ( 1041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 659 MET cc_start: 0.8792 (mmm) cc_final: 0.8556 (mmm) outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 0.0611 time to fit residues: 5.0553 Evaluate side-chains 48 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 479 ASN B 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.058922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.039062 restraints weight = 49517.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.040235 restraints weight = 24928.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.040960 restraints weight = 16065.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.041394 restraints weight = 12219.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.041616 restraints weight = 10297.529| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7274 Z= 0.144 Angle : 0.539 5.925 9799 Z= 0.276 Chirality : 0.040 0.140 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.561 32.958 966 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.65 % Allowed : 9.75 % Favored : 89.60 % 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: 0.76 (0.29), residues: 876 helix: 1.79 (0.25), residues: 471 sheet: -0.56 (0.71), residues: 67 loop : -1.15 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.010 0.001 TYR B 178 PHE 0.020 0.001 PHE A 46 TRP 0.006 0.001 TRP A 130 HIS 0.005 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7274) covalent geometry : angle 0.53913 ( 9799) hydrogen bonds : bond 0.03167 ( 355) hydrogen bonds : angle 4.52107 ( 1041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.9137 (pmm) cc_final: 0.8900 (pmm) REVERT: A 659 MET cc_start: 0.8819 (mmm) cc_final: 0.8465 (mmm) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.0622 time to fit residues: 4.9221 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS A 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.057653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037795 restraints weight = 47471.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.038991 restraints weight = 24122.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.039751 restraints weight = 15339.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.040218 restraints weight = 11395.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.040513 restraints weight = 9454.615| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7274 Z= 0.150 Angle : 0.538 6.078 9799 Z= 0.274 Chirality : 0.040 0.143 1064 Planarity : 0.003 0.033 1270 Dihedral : 4.594 32.975 966 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 10.79 % Favored : 87.78 % 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: 0.75 (0.29), residues: 876 helix: 1.81 (0.25), residues: 472 sheet: -0.67 (0.70), residues: 69 loop : -1.17 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR B 178 PHE 0.011 0.001 PHE A 359 TRP 0.006 0.001 TRP A 508 HIS 0.005 0.001 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7274) covalent geometry : angle 0.53845 ( 9799) hydrogen bonds : bond 0.03030 ( 355) hydrogen bonds : angle 4.36001 ( 1041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 539 MET cc_start: 0.8266 (mmt) cc_final: 0.8055 (mmt) REVERT: A 659 MET cc_start: 0.8849 (mmm) cc_final: 0.8530 (mmm) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.0748 time to fit residues: 6.3650 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.057558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.037635 restraints weight = 47086.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.038842 restraints weight = 23974.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.039593 restraints weight = 15246.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.040038 restraints weight = 11391.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.040300 restraints weight = 9458.377| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7274 Z= 0.137 Angle : 0.527 6.043 9799 Z= 0.271 Chirality : 0.040 0.140 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.527 32.420 965 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.91 % Allowed : 12.74 % Favored : 86.35 % 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: 0.76 (0.29), residues: 876 helix: 1.82 (0.25), residues: 472 sheet: -0.73 (0.69), residues: 69 loop : -1.16 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.011 0.001 TYR B 178 PHE 0.019 0.001 PHE A 46 TRP 0.007 0.001 TRP A 508 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7274) covalent geometry : angle 0.52736 ( 9799) hydrogen bonds : bond 0.02957 ( 355) hydrogen bonds : angle 4.30015 ( 1041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7335 (m-80) cc_final: 0.6990 (m-80) REVERT: A 535 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8824 (mm-30) REVERT: A 539 MET cc_start: 0.8286 (mmt) cc_final: 0.8080 (mmt) REVERT: A 659 MET cc_start: 0.8878 (mmm) cc_final: 0.8487 (mmm) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.0695 time to fit residues: 5.8322 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.056533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036726 restraints weight = 49146.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.037848 restraints weight = 24987.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038550 restraints weight = 16126.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038966 restraints weight = 12210.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.039221 restraints weight = 10317.812| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7274 Z= 0.214 Angle : 0.602 7.901 9799 Z= 0.311 Chirality : 0.041 0.148 1064 Planarity : 0.004 0.038 1270 Dihedral : 4.873 37.221 965 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.82 % Allowed : 13.39 % Favored : 84.79 % 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: 0.47 (0.29), residues: 876 helix: 1.65 (0.25), residues: 472 sheet: -1.26 (0.65), residues: 77 loop : -1.30 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 169 TYR 0.013 0.002 TYR A 194 PHE 0.016 0.002 PHE A 510 TRP 0.006 0.001 TRP A 130 HIS 0.004 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7274) covalent geometry : angle 0.60250 ( 9799) hydrogen bonds : bond 0.03311 ( 355) hydrogen bonds : angle 4.56555 ( 1041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8651 (pmm) cc_final: 0.8419 (pmm) REVERT: A 195 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: A 539 MET cc_start: 0.8271 (mmt) cc_final: 0.8050 (mmt) REVERT: A 659 MET cc_start: 0.8808 (mmm) cc_final: 0.8496 (mmm) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 0.0680 time to fit residues: 5.7785 Evaluate side-chains 51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.0070 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.057221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037504 restraints weight = 47078.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.038707 restraints weight = 23579.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.039421 restraints weight = 15023.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.039910 restraints weight = 11272.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.040176 restraints weight = 9394.674| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7274 Z= 0.118 Angle : 0.559 12.036 9799 Z= 0.279 Chirality : 0.040 0.135 1064 Planarity : 0.003 0.033 1270 Dihedral : 4.607 32.998 965 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 14.17 % Favored : 84.40 % 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: 0.60 (0.29), residues: 876 helix: 1.74 (0.25), residues: 472 sheet: -1.17 (0.64), residues: 79 loop : -1.21 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.011 0.001 TYR B 178 PHE 0.024 0.001 PHE A 46 TRP 0.004 0.001 TRP A 112 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7274) covalent geometry : angle 0.55947 ( 9799) hydrogen bonds : bond 0.02980 ( 355) hydrogen bonds : angle 4.35554 ( 1041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7446 (m-80) cc_final: 0.7171 (m-80) REVERT: A 92 MET cc_start: 0.8561 (pmm) cc_final: 0.8342 (pmm) REVERT: A 195 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: A 659 MET cc_start: 0.8780 (mmm) cc_final: 0.8380 (mmm) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 0.0601 time to fit residues: 4.9438 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 40 optimal weight: 0.0980 chunk 61 optimal weight: 0.0270 chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 222 GLN ** A 692 GLN ** 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 = 0.3670 r_free = 0.3670 target = 0.057705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.037855 restraints weight = 49078.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039029 restraints weight = 24464.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.039767 restraints weight = 15728.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.040215 restraints weight = 11834.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.040454 restraints weight = 9915.925| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7274 Z= 0.119 Angle : 0.553 11.985 9799 Z= 0.275 Chirality : 0.040 0.137 1064 Planarity : 0.003 0.032 1270 Dihedral : 4.509 31.189 965 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.43 % Allowed : 14.04 % Favored : 84.53 % 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: 0.65 (0.29), residues: 876 helix: 1.77 (0.25), residues: 472 sheet: -1.10 (0.65), residues: 79 loop : -1.18 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.011 0.001 TYR B 178 PHE 0.020 0.001 PHE A 46 TRP 0.003 0.001 TRP A 508 HIS 0.003 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7274) covalent geometry : angle 0.55299 ( 9799) hydrogen bonds : bond 0.02843 ( 355) hydrogen bonds : angle 4.32659 ( 1041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7440 (m-80) cc_final: 0.7192 (m-80) REVERT: A 92 MET cc_start: 0.8575 (pmm) cc_final: 0.8352 (pmm) REVERT: A 195 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: A 659 MET cc_start: 0.8790 (mmm) cc_final: 0.8467 (mmm) REVERT: B 97 MET cc_start: 0.2674 (tpt) cc_final: 0.2449 (tmm) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.0762 time to fit residues: 6.1512 Evaluate side-chains 55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 0.1980 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.057768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038102 restraints weight = 48472.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.039171 restraints weight = 24228.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.039861 restraints weight = 15639.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.040315 restraints weight = 11854.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.040575 restraints weight = 9933.705| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7274 Z= 0.113 Angle : 0.568 12.349 9799 Z= 0.278 Chirality : 0.040 0.167 1064 Planarity : 0.003 0.032 1270 Dihedral : 4.444 30.714 965 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.43 % Allowed : 14.69 % Favored : 83.88 % 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: 0.70 (0.30), residues: 876 helix: 1.82 (0.25), residues: 462 sheet: -1.05 (0.65), residues: 79 loop : -1.09 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.010 0.001 TYR B 178 PHE 0.019 0.001 PHE A 46 TRP 0.028 0.002 TRP A 508 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7274) covalent geometry : angle 0.56787 ( 9799) hydrogen bonds : bond 0.02831 ( 355) hydrogen bonds : angle 4.31281 ( 1041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7438 (m-80) cc_final: 0.7175 (m-80) REVERT: A 92 MET cc_start: 0.8582 (pmm) cc_final: 0.8331 (pmm) REVERT: A 195 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: A 515 MET cc_start: 0.8726 (ptp) cc_final: 0.8523 (pmm) REVERT: A 659 MET cc_start: 0.8821 (mmm) cc_final: 0.8470 (mmm) REVERT: B 97 MET cc_start: 0.2680 (tpt) cc_final: 0.2447 (tmm) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.0707 time to fit residues: 5.7810 Evaluate side-chains 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.056883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.037780 restraints weight = 50522.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.038888 restraints weight = 25610.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.039566 restraints weight = 16592.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039982 restraints weight = 12635.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.040217 restraints weight = 10761.649| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7274 Z= 0.169 Angle : 0.618 11.913 9799 Z= 0.307 Chirality : 0.041 0.215 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.654 33.291 965 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.56 % Allowed : 14.95 % Favored : 83.49 % 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: 0.62 (0.29), residues: 876 helix: 1.71 (0.25), residues: 468 sheet: -0.66 (0.71), residues: 67 loop : -1.23 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.011 0.001 TYR A 194 PHE 0.017 0.001 PHE A 46 TRP 0.033 0.002 TRP A 508 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7274) covalent geometry : angle 0.61768 ( 9799) hydrogen bonds : bond 0.03036 ( 355) hydrogen bonds : angle 4.44251 ( 1041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8600 (pmm) cc_final: 0.8381 (pmm) REVERT: A 195 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: A 493 MET cc_start: 0.9307 (tpp) cc_final: 0.8787 (tpp) REVERT: A 659 MET cc_start: 0.8688 (mmm) cc_final: 0.8340 (mmm) REVERT: B 97 MET cc_start: 0.2831 (tpt) cc_final: 0.2585 (tmm) outliers start: 12 outliers final: 11 residues processed: 55 average time/residue: 0.0753 time to fit residues: 5.9374 Evaluate side-chains 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 142 TYR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 49 optimal weight: 0.0470 chunk 9 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 53 optimal weight: 0.0570 chunk 62 optimal weight: 0.3980 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038532 restraints weight = 50040.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.039684 restraints weight = 25095.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.040364 restraints weight = 16009.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.040842 restraints weight = 12161.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.041076 restraints weight = 10218.964| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7274 Z= 0.100 Angle : 0.580 12.312 9799 Z= 0.283 Chirality : 0.040 0.186 1064 Planarity : 0.003 0.033 1270 Dihedral : 4.403 31.512 965 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.30 % Allowed : 15.73 % Favored : 82.96 % 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: 0.69 (0.30), residues: 876 helix: 1.79 (0.25), residues: 465 sheet: -1.03 (0.65), residues: 79 loop : -1.10 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.009 0.001 TYR B 178 PHE 0.011 0.001 PHE A 764 TRP 0.019 0.001 TRP A 508 HIS 0.004 0.001 HIS A 97 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7274) covalent geometry : angle 0.58028 ( 9799) hydrogen bonds : bond 0.02735 ( 355) hydrogen bonds : angle 4.25709 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.93 seconds wall clock time: 28 minutes 4.15 seconds (1684.15 seconds total)