Starting phenix.real_space_refine on Tue Aug 4 20:18:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v66_64798/08_2026/9v66_64798.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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 18 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 4007 2.51 5 N 1180 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6068 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 42, 'TRANS': 717} Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 6} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.74, per 1000 atoms: 0.27 Number of scatterers: 6456 At special positions: 0 Unit cell: (83.398, 94.461, 99.567, 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 15 16.00 P 18 15.00 Mg 1 11.99 O 1235 8.00 N 1180 7.00 C 4007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 327.3 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 31.7% alpha, 28.3% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.566A pdb=" N ALA A 108 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 325 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 372 through 392 removed outlier: 3.777A pdb=" N LYS A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N MET A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 516 through 530 Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 621 through 639 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.510A pdb=" N GLN A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 749 through 753 removed outlier: 3.531A pdb=" N ARG A 753 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.868A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR A 185 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE A 232 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 276 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 272 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.868A pdb=" N LEU A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG A 162 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 174 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 330 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.367A pdb=" N ALA A 67 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 26 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU A 23 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLU A 99 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL A 25 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 97 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA6, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 442 removed outlier: 7.159A pdb=" N LEU A 402 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE A 440 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 404 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR A 442 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 406 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 401 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 472 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A 403 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL A 474 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 405 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 568 through 575 removed outlier: 6.369A pdb=" N PHE A 545 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS A 615 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET A 547 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP A 617 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL A 549 " --> pdb=" O ASP A 617 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 612 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 650 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 614 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 652 " --> pdb=" O VAL A 614 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG A 616 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 649 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 679 " --> pdb=" O THR A 691 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.75 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: 1972 1.34 - 1.45: 1009 1.45 - 1.57: 3586 1.57 - 1.69: 35 1.69 - 1.81: 23 Bond restraints: 6625 Sorted by residual: bond pdb=" C3' DT B 16 " pdb=" C2' DT B 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.55e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 bond pdb=" C3' DT B 13 " pdb=" C2' DT B 13 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.24e+00 bond pdb=" C3' DT B 16 " pdb=" O3' DT B 16 " ideal model delta sigma weight residual 1.435 1.464 -0.029 1.30e-02 5.92e+03 4.95e+00 bond pdb=" O4' DG B 12 " pdb=" C1' DG B 12 " ideal model delta sigma weight residual 1.420 1.397 0.023 1.10e-02 8.26e+03 4.56e+00 ... (remaining 6620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 8898 1.51 - 3.02: 149 3.02 - 4.52: 19 4.52 - 6.03: 4 6.03 - 7.54: 3 Bond angle restraints: 9073 Sorted by residual: angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT B 18 " pdb=" C4 DT B 18 " pdb=" O4 DT B 18 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT B 16 " pdb=" C4 DT B 16 " pdb=" O4 DT B 16 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 ... (remaining 9068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 3804 33.97 - 67.93: 131 67.93 - 101.89: 6 101.89 - 135.86: 1 135.86 - 169.82: 1 Dihedral angle restraints: 3943 sinusoidal: 1751 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT B 16 " pdb=" C3' DT B 16 " pdb=" O3' DT B 16 " pdb=" P DA B 17 " ideal model delta sinusoidal sigma weight residual 220.00 50.18 169.82 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG B 15 " pdb=" C3' DG B 15 " pdb=" O3' DG B 15 " pdb=" P DT B 16 " ideal model delta sinusoidal sigma weight residual 220.00 84.36 135.64 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA ASP A 329 " pdb=" CB ASP A 329 " pdb=" CG ASP A 329 " pdb=" OD1 ASP A 329 " ideal model delta sinusoidal sigma weight residual -30.00 -85.63 55.63 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 3940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 973 0.109 - 0.218: 21 0.218 - 0.326: 0 0.326 - 0.435: 1 0.435 - 0.544: 2 Chirality restraints: 997 Sorted by residual: chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" P DA B 3 " pdb=" OP1 DA B 3 " pdb=" OP2 DA B 3 " pdb=" O5' DA B 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" P DG B 2 " pdb=" OP1 DG B 2 " pdb=" OP2 DG B 2 " pdb=" O5' DG B 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 994 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 533 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 534 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 607 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 608 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 608 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 608 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 2 " 0.018 2.00e-02 2.50e+03 7.18e-03 1.55e+00 pdb=" N9 DG B 2 " -0.011 2.00e-02 2.50e+03 pdb=" C8 DG B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG B 2 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG B 2 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG B 2 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG B 2 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DG B 2 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG B 2 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG B 2 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG B 2 " -0.006 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 5616 3.24 - 3.79: 9732 3.79 - 4.35: 13257 4.35 - 4.90: 22152 Nonbonded interactions: 50884 Sorted by model distance: nonbonded pdb=" OE1 GLN A 497 " pdb="MG MG A 801 " model vdw 2.136 2.170 nonbonded pdb=" OG1 THR A 236 " pdb=" O ALA A 272 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 185 " pdb=" O VAL A 307 " model vdw 2.302 3.040 nonbonded pdb=" O TYR A 732 " pdb=" OG1 THR A 735 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 257 " pdb=" NH1 ARG A 261 " model vdw 2.309 3.120 ... (remaining 50879 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.550 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 0.034 6625 Z= 0.182 Angle : 0.492 7.539 9073 Z= 0.312 Chirality : 0.048 0.544 997 Planarity : 0.004 0.033 1127 Dihedral : 16.072 169.823 2531 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.15 % Allowed : 0.31 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 758 helix: 2.53 (0.35), residues: 219 sheet: 0.92 (0.38), residues: 192 loop : -0.12 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.009 0.001 TYR A 377 PHE 0.016 0.001 PHE A 469 TRP 0.008 0.001 TRP A 136 HIS 0.002 0.000 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.18 ( 6625) covalent geometry : angle 0.49223 / 0.31 ( 9073) hydrogen bonds : bond 0.18058 / 11.55 ( 261) hydrogen bonds : angle 6.49577 / 4.63 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.237 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.6144 time to fit residues: 48.4170 Evaluate side-chains 51 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A 420 GLN A 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.179350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127159 restraints weight = 6698.677| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.08 r_work: 0.3125 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6625 Z= 0.257 Angle : 0.646 9.600 9073 Z= 0.340 Chirality : 0.048 0.293 997 Planarity : 0.005 0.045 1127 Dihedral : 15.535 179.012 1045 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.85 % Allowed : 6.46 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.31), residues: 758 helix: 1.99 (0.34), residues: 227 sheet: 0.78 (0.39), residues: 186 loop : -0.38 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 157 TYR 0.021 0.002 TYR A 377 PHE 0.015 0.002 PHE A 545 TRP 0.013 0.002 TRP A 136 HIS 0.012 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 ( 6625) covalent geometry : angle 0.64602 / 0.34 ( 9073) hydrogen bonds : bond 0.05477 / 3.56 ( 261) hydrogen bonds : angle 4.99733 / 3.59 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.236 Fit side-chains REVERT: A 27 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.7027 (mmm-85) REVERT: A 150 ASN cc_start: 0.7824 (t0) cc_final: 0.7532 (t0) REVERT: A 174 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7951 (mptp) REVERT: A 698 ARG cc_start: 0.8084 (ttt-90) cc_final: 0.7866 (ttt-90) outliers start: 12 outliers final: 5 residues processed: 65 average time/residue: 0.5919 time to fit residues: 40.5102 Evaluate side-chains 60 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.181600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.129733 restraints weight = 6637.114| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.39 r_work: 0.3217 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6625 Z= 0.138 Angle : 0.506 5.426 9073 Z= 0.273 Chirality : 0.043 0.290 997 Planarity : 0.004 0.039 1127 Dihedral : 15.479 179.220 1045 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.69 % Allowed : 10.77 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.31), residues: 758 helix: 2.21 (0.34), residues: 227 sheet: 0.56 (0.37), residues: 206 loop : -0.36 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 255 TYR 0.016 0.001 TYR A 377 PHE 0.009 0.001 PHE A 545 TRP 0.012 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6625) covalent geometry : angle 0.50605 / 0.27 ( 9073) hydrogen bonds : bond 0.04176 / 2.74 ( 261) hydrogen bonds : angle 4.65701 / 3.34 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.247 Fit side-chains REVERT: A 121 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8052 (ttpt) REVERT: A 147 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: A 150 ASN cc_start: 0.7669 (t0) cc_final: 0.7357 (t0) REVERT: A 174 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7809 (mptp) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 0.5507 time to fit residues: 37.8038 Evaluate side-chains 63 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 420 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129399 restraints weight = 6772.394| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.10 r_work: 0.3151 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6625 Z= 0.224 Angle : 0.597 8.127 9073 Z= 0.315 Chirality : 0.046 0.305 997 Planarity : 0.005 0.048 1127 Dihedral : 15.518 178.198 1045 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.15 % Allowed : 12.46 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 758 helix: 1.96 (0.33), residues: 227 sheet: 0.46 (0.37), residues: 206 loop : -0.52 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 157 TYR 0.020 0.002 TYR A 377 PHE 0.013 0.002 PHE A 545 TRP 0.013 0.002 TRP A 136 HIS 0.011 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 ( 6625) covalent geometry : angle 0.59714 / 0.32 ( 9073) hydrogen bonds : bond 0.04957 / 3.28 ( 261) hydrogen bonds : angle 4.67862 / 3.35 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.163 Fit side-chains REVERT: A 121 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: A 147 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: A 150 ASN cc_start: 0.8037 (t0) cc_final: 0.7783 (t0) REVERT: A 174 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7939 (mptp) REVERT: A 490 ARG cc_start: 0.6796 (tpt-90) cc_final: 0.6549 (tpt90) outliers start: 14 outliers final: 7 residues processed: 68 average time/residue: 0.5903 time to fit residues: 42.2125 Evaluate side-chains 65 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 685 ASN A 702 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132345 restraints weight = 6810.034| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.10 r_work: 0.3191 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6625 Z= 0.135 Angle : 0.519 9.895 9073 Z= 0.276 Chirality : 0.043 0.297 997 Planarity : 0.004 0.041 1127 Dihedral : 15.495 176.720 1045 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.00 % Allowed : 14.31 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.31), residues: 758 helix: 2.15 (0.34), residues: 227 sheet: 0.51 (0.37), residues: 206 loop : -0.47 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.016 0.001 TYR A 377 PHE 0.010 0.001 PHE A 545 TRP 0.013 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6625) covalent geometry : angle 0.51869 / 0.28 ( 9073) hydrogen bonds : bond 0.03880 / 2.56 ( 261) hydrogen bonds : angle 4.49191 / 3.23 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.279 Fit side-chains REVERT: A 121 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8150 (ttpt) REVERT: A 147 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: A 174 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7881 (mptp) REVERT: A 490 ARG cc_start: 0.6821 (tpt-90) cc_final: 0.6573 (tpt-90) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 0.5705 time to fit residues: 39.7650 Evaluate side-chains 64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 24 optimal weight: 0.7980 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 304 ASN A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129473 restraints weight = 6790.122| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.22 r_work: 0.3154 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6625 Z= 0.186 Angle : 0.554 6.728 9073 Z= 0.294 Chirality : 0.045 0.308 997 Planarity : 0.004 0.044 1127 Dihedral : 15.501 176.006 1045 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.85 % Allowed : 15.08 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.30), residues: 758 helix: 2.11 (0.34), residues: 227 sheet: 0.48 (0.37), residues: 206 loop : -0.53 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 157 TYR 0.018 0.002 TYR A 377 PHE 0.017 0.002 PHE A 469 TRP 0.012 0.002 TRP A 136 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 6625) covalent geometry : angle 0.55418 / 0.29 ( 9073) hydrogen bonds : bond 0.04384 / 2.90 ( 261) hydrogen bonds : angle 4.49477 / 3.23 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.172 Fit side-chains REVERT: A 121 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8151 (ttpt) REVERT: A 147 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: A 174 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7927 (mptp) REVERT: A 490 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6582 (tpt-90) REVERT: A 573 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8158 (mtm-85) outliers start: 12 outliers final: 4 residues processed: 64 average time/residue: 0.5875 time to fit residues: 39.3779 Evaluate side-chains 60 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.185159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131610 restraints weight = 6757.241| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.22 r_work: 0.3213 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6625 Z= 0.121 Angle : 0.494 6.119 9073 Z= 0.266 Chirality : 0.043 0.302 997 Planarity : 0.004 0.039 1127 Dihedral : 15.480 174.313 1045 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.85 % Allowed : 15.23 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.31), residues: 758 helix: 2.29 (0.34), residues: 227 sheet: 0.54 (0.38), residues: 206 loop : -0.44 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 157 TYR 0.014 0.001 TYR A 377 PHE 0.016 0.001 PHE A 469 TRP 0.012 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 6625) covalent geometry : angle 0.49408 / 0.27 ( 9073) hydrogen bonds : bond 0.03524 / 2.32 ( 261) hydrogen bonds : angle 4.35251 / 3.13 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.261 Fit side-chains REVERT: A 121 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8139 (ttpt) REVERT: A 490 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.6554 (tpt-90) REVERT: A 573 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8185 (mtm-85) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.5860 time to fit residues: 38.9167 Evaluate side-chains 61 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131980 restraints weight = 6751.794| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.12 r_work: 0.3183 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6625 Z= 0.139 Angle : 0.513 6.326 9073 Z= 0.273 Chirality : 0.043 0.308 997 Planarity : 0.004 0.041 1127 Dihedral : 15.455 173.310 1045 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.54 % Allowed : 16.00 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.31), residues: 758 helix: 2.30 (0.34), residues: 227 sheet: 0.56 (0.37), residues: 206 loop : -0.45 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 157 TYR 0.015 0.001 TYR A 377 PHE 0.019 0.001 PHE A 469 TRP 0.011 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6625) covalent geometry : angle 0.51285 / 0.27 ( 9073) hydrogen bonds : bond 0.03727 / 2.46 ( 261) hydrogen bonds : angle 4.32637 / 3.11 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8169 (ttpt) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.5409 time to fit residues: 35.4720 Evaluate side-chains 60 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.184652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.132008 restraints weight = 6838.660| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.13 r_work: 0.3184 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6625 Z= 0.142 Angle : 0.516 6.762 9073 Z= 0.274 Chirality : 0.043 0.309 997 Planarity : 0.004 0.041 1127 Dihedral : 15.447 171.823 1045 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.69 % Allowed : 16.00 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.31), residues: 758 helix: 2.30 (0.34), residues: 227 sheet: 0.79 (0.39), residues: 186 loop : -0.50 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 157 TYR 0.015 0.001 TYR A 377 PHE 0.018 0.001 PHE A 469 TRP 0.011 0.001 TRP A 136 HIS 0.007 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6625) covalent geometry : angle 0.51644 / 0.27 ( 9073) hydrogen bonds : bond 0.03729 / 2.46 ( 261) hydrogen bonds : angle 4.32106 / 3.11 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (ttpt) REVERT: A 698 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7488 (ttp80) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.6003 time to fit residues: 36.7439 Evaluate side-chains 58 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 698 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 43 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.182659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.130581 restraints weight = 6740.725| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.15 r_work: 0.3185 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6625 Z= 0.189 Angle : 0.566 6.992 9073 Z= 0.298 Chirality : 0.045 0.315 997 Planarity : 0.005 0.044 1127 Dihedral : 15.470 170.665 1045 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.69 % Allowed : 16.00 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.30), residues: 758 helix: 2.12 (0.34), residues: 228 sheet: 0.75 (0.39), residues: 186 loop : -0.59 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 157 TYR 0.019 0.002 TYR A 377 PHE 0.018 0.002 PHE A 469 TRP 0.009 0.002 TRP A 136 HIS 0.009 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 6625) covalent geometry : angle 0.56592 / 0.30 ( 9073) hydrogen bonds : bond 0.04347 / 2.87 ( 261) hydrogen bonds : angle 4.41840 / 3.18 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (ttpt) REVERT: A 238 LYS cc_start: 0.7700 (mtpp) cc_final: 0.7495 (mtpp) REVERT: A 698 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7518 (ttp80) outliers start: 11 outliers final: 5 residues processed: 59 average time/residue: 0.5830 time to fit residues: 36.2833 Evaluate side-chains 56 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 698 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130928 restraints weight = 6729.030| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.14 r_work: 0.3166 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6625 Z= 0.162 Angle : 0.542 6.982 9073 Z= 0.287 Chirality : 0.044 0.311 997 Planarity : 0.004 0.043 1127 Dihedral : 15.479 169.654 1045 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.69 % Allowed : 16.31 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 758 helix: 2.14 (0.34), residues: 228 sheet: 0.76 (0.39), residues: 186 loop : -0.57 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 157 TYR 0.016 0.001 TYR A 377 PHE 0.017 0.001 PHE A 469 TRP 0.011 0.001 TRP A 136 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 6625) covalent geometry : angle 0.54220 / 0.29 ( 9073) hydrogen bonds : bond 0.04050 / 2.67 ( 261) hydrogen bonds : angle 4.37999 / 3.15 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.26 seconds wall clock time: 32 minutes 50.51 seconds (1970.51 seconds total)