Starting phenix.real_space_refine on Wed Mar 12 05:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8efe_28081/03_2025/8efe_28081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8efe_28081/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8efe_28081/03_2025/8efe_28081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8efe_28081/03_2025/8efe_28081.map" model { file = "/net/cci-nas-00/data/ceres_data/8efe_28081/03_2025/8efe_28081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8efe_28081/03_2025/8efe_28081.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.73, per 1000 atoms: 0.80 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: 1.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.23 Time building geometry restraints manager: 1.98 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: 91.430 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.600 ------------------------------------------------------------------------------- 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= 0.148 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 : 8.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (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 TRP 0.021 0.002 TRP A 112 HIS 0.002 0.000 HIS A 153 PHE 0.019 0.001 PHE A 46 TYR 0.013 0.001 TYR A 194 ARG 0.002 0.000 ARG A 272 *********************** 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 : 0.882 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: 0.2184 time to fit residues: 18.4017 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 : 0.791 ------------------------------------------------------------------------------- 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 74 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS B 91 ASN B 184 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.058580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.038808 restraints weight = 46236.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.039972 restraints weight = 23404.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.040724 restraints weight = 14843.713| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1224 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= 0.226 Angle : 0.570 6.075 9799 Z= 0.294 Chirality : 0.041 0.150 1064 Planarity : 0.004 0.036 1270 Dihedral : 4.534 36.622 966 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 876 helix: 1.91 (0.25), residues: 470 sheet: -0.68 (0.69), residues: 67 loop : -1.10 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.004 0.001 HIS A 668 PHE 0.011 0.001 PHE A 764 TYR 0.013 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** 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 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 659 MET cc_start: 0.8750 (mmm) cc_final: 0.8512 (mmm) REVERT: A 776 MET cc_start: 0.9716 (ttm) cc_final: 0.9515 (ptm) outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 0.2043 time to fit residues: 16.7523 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 : 0.845 ------------------------------------------------------------------------------- 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 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 372 GLN A 479 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.058655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.038620 restraints weight = 47630.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039806 restraints weight = 24352.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.040531 restraints weight = 15791.607| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1570 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= 0.183 Angle : 0.526 5.936 9799 Z= 0.270 Chirality : 0.040 0.150 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.495 31.959 966 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.52 % Allowed : 9.75 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 876 helix: 1.82 (0.25), residues: 471 sheet: -0.51 (0.72), residues: 67 loop : -1.17 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 130 HIS 0.008 0.001 HIS B 148 PHE 0.017 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.003 0.000 ARG A 169 *********************** 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: 4 poor density : 51 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 MET cc_start: 0.8738 (mmm) cc_final: 0.8414 (mmm) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.1685 time to fit residues: 13.0795 Evaluate side-chains 51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR 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 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.058141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.038221 restraints weight = 46548.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.039398 restraints weight = 23465.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.040182 restraints weight = 14988.996| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1815 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= 0.193 Angle : 0.527 6.238 9799 Z= 0.268 Chirality : 0.040 0.142 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.465 31.381 966 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.91 % Allowed : 10.92 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 876 helix: 1.89 (0.25), residues: 466 sheet: -0.45 (0.72), residues: 67 loop : -1.12 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 508 HIS 0.004 0.001 HIS B 148 PHE 0.009 0.001 PHE A 359 TYR 0.010 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** 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 58 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.9220 (pmm) cc_final: 0.9001 (pmm) REVERT: A 539 MET cc_start: 0.8295 (mmt) cc_final: 0.8087 (mmt) REVERT: A 659 MET cc_start: 0.8859 (mmm) cc_final: 0.8544 (mmm) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1791 time to fit residues: 14.7659 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 : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.058033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038149 restraints weight = 46560.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039350 restraints weight = 23621.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.040094 restraints weight = 14982.856| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2035 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= 0.185 Angle : 0.521 6.185 9799 Z= 0.266 Chirality : 0.039 0.139 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.391 31.180 965 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.30 % Allowed : 12.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 876 helix: 1.89 (0.25), residues: 467 sheet: -0.57 (0.71), residues: 69 loop : -1.12 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 508 HIS 0.005 0.001 HIS B 148 PHE 0.019 0.001 PHE A 46 TYR 0.010 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** 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 62 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8809 (mm-30) REVERT: A 659 MET cc_start: 0.8788 (mmm) cc_final: 0.8443 (mmm) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.1788 time to fit residues: 15.7714 Evaluate side-chains 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.057777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.037906 restraints weight = 47534.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.039075 restraints weight = 24155.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.039813 restraints weight = 15434.582| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2226 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= 0.189 Angle : 0.531 6.764 9799 Z= 0.270 Chirality : 0.039 0.141 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.418 31.530 965 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.43 % Allowed : 13.00 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 876 helix: 1.86 (0.25), residues: 467 sheet: -0.63 (0.70), residues: 69 loop : -1.14 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.004 0.001 HIS B 148 PHE 0.009 0.001 PHE A 312 TYR 0.010 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** 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 60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8821 (mm-30) REVERT: A 659 MET cc_start: 0.8835 (mmm) cc_final: 0.8447 (mmm) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 0.1791 time to fit residues: 15.2177 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 672 CYS 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 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 56 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.058196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.038341 restraints weight = 46388.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.039559 restraints weight = 23361.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.040302 restraints weight = 14843.713| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7274 Z= 0.155 Angle : 0.531 6.574 9799 Z= 0.266 Chirality : 0.039 0.135 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.314 30.973 965 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.91 % Allowed : 14.04 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 876 helix: 1.82 (0.25), residues: 467 sheet: -0.57 (0.70), residues: 69 loop : -1.10 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 508 HIS 0.003 0.001 HIS B 148 PHE 0.009 0.001 PHE A 764 TYR 0.018 0.001 TYR B 123 ARG 0.002 0.000 ARG A 169 *********************** 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 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.8814 (ptp) cc_final: 0.8561 (pmm) REVERT: A 535 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8772 (mm-30) REVERT: A 659 MET cc_start: 0.8794 (mmm) cc_final: 0.8430 (mmm) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1729 time to fit residues: 14.0768 Evaluate side-chains 52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.057456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.037752 restraints weight = 48059.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.038851 restraints weight = 24586.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.039591 restraints weight = 15983.404| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2461 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= 0.192 Angle : 0.542 7.020 9799 Z= 0.274 Chirality : 0.040 0.158 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.371 31.128 965 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.30 % Allowed : 13.78 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 876 helix: 1.82 (0.25), residues: 467 sheet: -0.60 (0.70), residues: 69 loop : -1.15 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 508 HIS 0.003 0.001 HIS A 97 PHE 0.011 0.001 PHE A 510 TYR 0.010 0.001 TYR B 178 ARG 0.003 0.000 ARG A 169 *********************** 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 57 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8556 (pmm) cc_final: 0.8319 (pmm) REVERT: A 535 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8799 (mm-30) REVERT: A 659 MET cc_start: 0.8826 (mmm) cc_final: 0.8463 (mmm) REVERT: B 97 MET cc_start: 0.2841 (tpt) cc_final: 0.2569 (tmm) outliers start: 10 outliers final: 8 residues processed: 56 average time/residue: 0.1749 time to fit residues: 14.3006 Evaluate side-chains 54 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 142 TYR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 11 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.057317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038044 restraints weight = 50686.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.039170 restraints weight = 25997.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.039829 restraints weight = 16862.532| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7274 Z= 0.258 Angle : 0.588 7.516 9799 Z= 0.298 Chirality : 0.041 0.144 1064 Planarity : 0.003 0.032 1270 Dihedral : 4.645 34.402 965 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.56 % Allowed : 13.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 876 helix: 1.74 (0.25), residues: 467 sheet: -0.64 (0.70), residues: 69 loop : -1.25 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 508 HIS 0.004 0.001 HIS A 97 PHE 0.013 0.001 PHE A 46 TYR 0.012 0.002 TYR A 194 ARG 0.004 0.000 ARG A 169 *********************** 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: 12 poor density : 47 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.7341 (m-80) cc_final: 0.7093 (m-80) REVERT: A 92 MET cc_start: 0.8601 (pmm) cc_final: 0.8395 (pmm) REVERT: A 195 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: A 659 MET cc_start: 0.8715 (mmm) cc_final: 0.8436 (mmm) REVERT: B 97 MET cc_start: 0.3183 (tpt) cc_final: 0.2912 (tmm) outliers start: 12 outliers final: 10 residues processed: 57 average time/residue: 0.1616 time to fit residues: 13.7247 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 : 0.837 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 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 222 GLN A 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.057101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.037342 restraints weight = 48040.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.038482 restraints weight = 24247.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039187 restraints weight = 15464.569| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2782 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= 0.204 Angle : 0.578 10.912 9799 Z= 0.290 Chirality : 0.040 0.188 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.548 32.848 965 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.43 % Allowed : 14.56 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 876 helix: 1.75 (0.25), residues: 471 sheet: -1.09 (0.65), residues: 79 loop : -1.20 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 508 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE A 312 TYR 0.011 0.001 TYR B 178 ARG 0.004 0.000 ARG B 58 ********************** 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 56 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8574 (pmm) cc_final: 0.8307 (pmm) REVERT: A 195 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: A 659 MET cc_start: 0.8896 (mmm) cc_final: 0.8470 (mmm) REVERT: B 97 MET cc_start: 0.2776 (tpt) cc_final: 0.2530 (tmm) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1635 time to fit residues: 12.8682 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 : 0.875 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.057541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.037785 restraints weight = 47586.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.038900 restraints weight = 24140.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.039655 restraints weight = 15546.763| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7274 Z= 0.188 Angle : 0.569 10.802 9799 Z= 0.283 Chirality : 0.040 0.170 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.491 31.413 965 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.30 % Allowed : 14.69 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 876 helix: 1.85 (0.25), residues: 465 sheet: -1.03 (0.65), residues: 79 loop : -1.14 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 508 HIS 0.004 0.001 HIS A 97 PHE 0.011 0.001 PHE A 312 TYR 0.010 0.001 TYR B 178 ARG 0.003 0.000 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3419.99 seconds wall clock time: 60 minutes 5.45 seconds (3605.45 seconds total)