Starting phenix.real_space_refine on Tue Sep 24 07:26:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_28081.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_28081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_28081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_28081.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/09_2024/8efe_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-5461/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: 5.30, per 1000 atoms: 0.74 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: 1.75 Conformation dependent library (CDL) restraints added in 926.3 milliseconds 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: 0.82 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: 2.13 Time building geometry restraints manager: 2.05 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: 6.550 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.822 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: 0.2158 time to fit residues: 18.2664 Evaluate side-chains 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1217 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= 0.228 Angle : 0.571 6.076 9799 Z= 0.294 Chirality : 0.041 0.149 1064 Planarity : 0.004 0.037 1270 Dihedral : 4.530 36.661 966 Min Nonbonded Distance : 1.832 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 0.010 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 fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 659 MET cc_start: 0.8927 (mmm) cc_final: 0.8663 (mmm) outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 0.1905 time to fit residues: 15.5691 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 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 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7274 Z= 0.220 Angle : 0.545 5.962 9799 Z= 0.280 Chirality : 0.040 0.152 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.613 33.442 966 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (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: 0.70 (0.29), residues: 876 helix: 1.77 (0.25), residues: 471 sheet: -0.57 (0.71), residues: 67 loop : -1.24 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 130 HIS 0.005 0.001 HIS B 148 PHE 0.010 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.004 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 fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.9147 (pmm) cc_final: 0.8918 (pmm) REVERT: A 659 MET cc_start: 0.8896 (mmm) cc_final: 0.8522 (mmm) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.1738 time to fit residues: 13.4382 Evaluate side-chains 52 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 79 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1832 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= 0.182 Angle : 0.523 6.234 9799 Z= 0.266 Chirality : 0.040 0.139 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.506 31.370 966 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.91 % Allowed : 11.31 % 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 (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: 1.83 (0.25), residues: 471 sheet: -0.61 (0.70), residues: 69 loop : -1.17 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 508 HIS 0.004 0.001 HIS B 148 PHE 0.011 0.001 PHE A 46 TYR 0.010 0.001 TYR B 178 ARG 0.003 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 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8772 (mm-30) REVERT: A 539 MET cc_start: 0.8266 (mmt) cc_final: 0.8061 (mmt) REVERT: A 659 MET cc_start: 0.8901 (mmm) cc_final: 0.8569 (mmm) outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1901 time to fit residues: 15.8693 Evaluate side-chains 55 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 B residue 184 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2000 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= 0.206 Angle : 0.536 6.244 9799 Z= 0.273 Chirality : 0.040 0.140 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.489 32.013 965 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.17 % Allowed : 13.00 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 876 helix: 1.86 (0.25), residues: 467 sheet: -0.65 (0.70), residues: 69 loop : -1.13 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 508 HIS 0.008 0.001 HIS B 148 PHE 0.013 0.001 PHE A 46 TYR 0.011 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 fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8793 (mm-30) REVERT: A 659 MET cc_start: 0.8928 (mmm) cc_final: 0.8554 (mmm) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1798 time to fit residues: 15.6096 Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 76 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2220 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= 0.182 Angle : 0.535 6.679 9799 Z= 0.272 Chirality : 0.039 0.138 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.456 31.288 965 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.30 % Allowed : 14.04 % Favored : 84.66 % 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: 0.81 (0.29), residues: 876 helix: 1.87 (0.25), residues: 467 sheet: -0.64 (0.69), residues: 69 loop : -1.12 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 112 HIS 0.005 0.001 HIS B 148 PHE 0.012 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.003 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 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8789 (mm-30) REVERT: A 659 MET cc_start: 0.8944 (mmm) cc_final: 0.8524 (mmm) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1820 time to fit residues: 15.2434 Evaluate side-chains 55 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 457 ILE 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 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7274 Z= 0.198 Angle : 0.550 7.099 9799 Z= 0.278 Chirality : 0.040 0.142 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.513 32.069 965 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.69 % Allowed : 13.65 % Favored : 84.66 % 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: 1.85 (0.25), residues: 467 sheet: -0.62 (0.69), residues: 69 loop : -1.15 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.004 0.001 HIS B 148 PHE 0.014 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.004 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 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8545 (pmm) cc_final: 0.8327 (pmm) REVERT: A 195 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: A 535 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8791 (mm-30) REVERT: A 659 MET cc_start: 0.8946 (mmm) cc_final: 0.8540 (mmm) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.1707 time to fit residues: 14.7755 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 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 B residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 74 optimal weight: 0.1980 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7274 Z= 0.143 Angle : 0.541 7.409 9799 Z= 0.272 Chirality : 0.039 0.151 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.339 31.215 965 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.17 % Allowed : 14.43 % 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 (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: 0.82 (0.29), residues: 876 helix: 1.88 (0.25), residues: 462 sheet: -0.56 (0.70), residues: 69 loop : -1.10 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 508 HIS 0.004 0.001 HIS A 97 PHE 0.026 0.001 PHE A 46 TYR 0.010 0.001 TYR B 178 ARG 0.002 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 58 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8501 (pmm) cc_final: 0.8243 (pmm) REVERT: A 195 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: A 515 MET cc_start: 0.8898 (ptp) cc_final: 0.8612 (pmm) REVERT: A 535 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8773 (mm-30) REVERT: A 659 MET cc_start: 0.8921 (mmm) cc_final: 0.8505 (mmm) REVERT: B 97 MET cc_start: 0.2527 (tpt) cc_final: 0.2314 (tmm) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.1737 time to fit residues: 14.0284 Evaluate side-chains 53 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 B residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7274 Z= 0.228 Angle : 0.586 7.508 9799 Z= 0.297 Chirality : 0.041 0.193 1064 Planarity : 0.003 0.028 1270 Dihedral : 4.534 32.554 965 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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 (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: 0.75 (0.29), residues: 876 helix: 1.83 (0.25), residues: 467 sheet: -0.54 (0.70), residues: 69 loop : -1.19 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 508 HIS 0.004 0.001 HIS B 148 PHE 0.040 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.003 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 fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8562 (pmm) cc_final: 0.8299 (pmm) REVERT: A 195 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 659 MET cc_start: 0.8962 (mmm) cc_final: 0.8608 (mmm) REVERT: B 97 MET cc_start: 0.2544 (tpt) cc_final: 0.2313 (tmm) REVERT: B 118 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8210 (pptt) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1835 time to fit residues: 15.1716 Evaluate side-chains 56 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 356 ILE 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 B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 7 optimal weight: 0.0170 chunk 53 optimal weight: 0.0570 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.0970 chunk 74 optimal weight: 0.6980 overall best weight: 0.1012 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7274 Z= 0.141 Angle : 0.571 11.102 9799 Z= 0.283 Chirality : 0.039 0.167 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.257 32.305 965 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.39 % Allowed : 15.99 % Favored : 83.62 % 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: 1.86 (0.25), residues: 464 sheet: -0.28 (0.70), residues: 67 loop : -1.12 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 508 HIS 0.005 0.001 HIS A 97 PHE 0.040 0.001 PHE A 46 TYR 0.010 0.001 TYR B 178 ARG 0.003 0.000 ARG A 108 ********************** 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 52 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.8498 (pmm) cc_final: 0.8241 (pmm) REVERT: A 535 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8824 (mm-30) REVERT: A 659 MET cc_start: 0.8910 (mmm) cc_final: 0.8529 (mmm) REVERT: B 118 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8141 (pptt) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1705 time to fit residues: 13.2587 Evaluate side-chains 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 359 PHE 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 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.058128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.039329 restraints weight = 49541.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.040457 restraints weight = 24519.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.041156 restraints weight = 15615.011| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.034 7274 Z= 0.219 Angle : 0.589 10.687 9799 Z= 0.293 Chirality : 0.040 0.166 1064 Planarity : 0.003 0.028 1270 Dihedral : 4.421 30.485 965 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.65 % Allowed : 16.12 % Favored : 83.22 % 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 (0.30), residues: 876 helix: 1.89 (0.25), residues: 469 sheet: -0.49 (0.70), residues: 69 loop : -1.13 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 508 HIS 0.003 0.001 HIS B 148 PHE 0.013 0.001 PHE A 46 TYR 0.009 0.001 TYR B 178 ARG 0.005 0.000 ARG B 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.24 seconds wall clock time: 32 minutes 53.59 seconds (1973.59 seconds total)