Starting phenix.real_space_refine on Thu Jul 2 04:21:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v66_64798/07_2026/9v66_64798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v66_64798/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9v66_64798/07_2026/9v66_64798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v66_64798/07_2026/9v66_64798.map" model { file = "/net/cci-nas-00/data/ceres_data/9v66_64798/07_2026/9v66_64798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v66_64798/07_2026/9v66_64798.cif" } 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-dev-6108/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: 1.46, per 1000 atoms: 0.23 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: 0.51 Conformation dependent library (CDL) restraints added in 341.1 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: 0.62 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: 0.83 Time building geometry restraints manager: 0.68 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- 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 : 0.491 7.539 9073 Z= 0.310 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 0.49073 / 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 : 0.236 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.5442 time to fit residues: 42.8760 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 : 0.144 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.179080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.126897 restraints weight = 6695.369| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.08 r_work: 0.3150 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6625 Z= 0.261 Angle : 0.655 10.151 9073 Z= 0.345 Chirality : 0.048 0.277 997 Planarity : 0.005 0.045 1127 Dihedral : 15.583 179.013 1045 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.85 % Allowed : 6.62 % Favored : 91.54 % 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: 0.86 (0.31), residues: 758 helix: 1.91 (0.34), residues: 227 sheet: 0.74 (0.39), residues: 186 loop : -0.40 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 463 TYR 0.022 0.002 TYR A 377 PHE 0.015 0.002 PHE A 545 TRP 0.014 0.002 TRP A 136 HIS 0.013 0.002 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.26 ( 6625) covalent geometry : angle 0.65520 / 0.35 ( 9073) hydrogen bonds : bond 0.05438 / 3.54 ( 261) hydrogen bonds : angle 4.98186 / 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 72 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.143 Fit side-chains REVERT: A 27 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6849 (mmm-85) REVERT: A 147 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: A 150 ASN cc_start: 0.7843 (t0) cc_final: 0.7594 (t0) REVERT: A 174 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7930 (mptp) REVERT: A 698 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7856 (ttt-90) outliers start: 12 outliers final: 5 residues processed: 66 average time/residue: 0.4970 time to fit residues: 34.5145 Evaluate side-chains 61 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 6.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.181581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.129660 restraints weight = 6632.788| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.41 r_work: 0.3219 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1234 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= 0.137 Angle : 0.502 5.077 9073 Z= 0.271 Chirality : 0.043 0.264 997 Planarity : 0.004 0.039 1127 Dihedral : 15.477 177.103 1045 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.54 % Allowed : 11.38 % Favored : 87.08 % 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: 0.97 (0.31), residues: 758 helix: 2.20 (0.34), residues: 227 sheet: 0.54 (0.37), residues: 206 loop : -0.37 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 255 TYR 0.015 0.001 TYR A 377 PHE 0.009 0.001 PHE A 545 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 0.00313 / 0.14 ( 6625) covalent geometry : angle 0.50167 / 0.27 ( 9073) hydrogen bonds : bond 0.04117 / 2.71 ( 261) hydrogen bonds : angle 4.63534 / 3.33 ( 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 69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.205 Fit side-chains REVERT: A 121 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8057 (ttpt) REVERT: A 150 ASN cc_start: 0.7695 (t0) cc_final: 0.7419 (t0) REVERT: A 174 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7817 (mptp) REVERT: A 490 ARG cc_start: 0.6611 (tpp80) cc_final: 0.6395 (tpt-90) outliers start: 10 outliers final: 4 residues processed: 67 average time/residue: 0.4901 time to fit residues: 34.6585 Evaluate side-chains 63 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS 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: 5.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131541 restraints weight = 6768.943| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.20 r_work: 0.3201 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1391 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= 0.137 Angle : 0.501 5.589 9073 Z= 0.268 Chirality : 0.043 0.273 997 Planarity : 0.004 0.040 1127 Dihedral : 15.449 175.666 1045 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.85 % Allowed : 12.77 % 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: 0.97 (0.31), residues: 758 helix: 2.26 (0.34), residues: 227 sheet: 0.56 (0.37), residues: 206 loop : -0.44 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.015 0.001 TYR A 377 PHE 0.010 0.001 PHE A 545 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 0.00318 / 0.14 ( 6625) covalent geometry : angle 0.50107 / 0.27 ( 9073) hydrogen bonds : bond 0.03829 / 2.52 ( 261) hydrogen bonds : angle 4.46670 / 3.22 ( 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 68 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.239 Fit side-chains REVERT: A 121 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8089 (ttpt) REVERT: A 147 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: A 150 ASN cc_start: 0.7721 (t0) cc_final: 0.7471 (t0) REVERT: A 174 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7852 (mptp) REVERT: A 490 ARG cc_start: 0.6645 (tpp80) cc_final: 0.6413 (tpt-90) outliers start: 12 outliers final: 4 residues processed: 63 average time/residue: 0.5425 time to fit residues: 36.1424 Evaluate side-chains 60 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 420 GLN A 685 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126561 restraints weight = 6830.440| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.07 r_work: 0.3182 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6625 Z= 0.213 Angle : 0.576 7.409 9073 Z= 0.305 Chirality : 0.045 0.283 997 Planarity : 0.005 0.045 1127 Dihedral : 15.487 174.432 1045 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.31 % Allowed : 13.38 % Favored : 84.31 % 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: 0.82 (0.31), residues: 758 helix: 2.08 (0.34), residues: 227 sheet: 0.49 (0.37), residues: 206 loop : -0.50 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 278 TYR 0.019 0.002 TYR A 377 PHE 0.011 0.002 PHE A 545 TRP 0.012 0.002 TRP A 136 HIS 0.010 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 ( 6625) covalent geometry : angle 0.57632 / 0.31 ( 9073) hydrogen bonds : bond 0.04696 / 3.11 ( 261) hydrogen bonds : angle 4.55745 / 3.28 ( 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 69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8230 (ttpt) REVERT: A 147 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 150 ASN cc_start: 0.8011 (t0) cc_final: 0.7731 (t0) outliers start: 15 outliers final: 7 residues processed: 65 average time/residue: 0.5464 time to fit residues: 37.5388 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 : 0.178 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 420 GLN A 439 GLN A 685 ASN A 702 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.184135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130667 restraints weight = 6786.659| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.20 r_work: 0.3192 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6625 Z= 0.147 Angle : 0.514 5.572 9073 Z= 0.276 Chirality : 0.043 0.278 997 Planarity : 0.004 0.042 1127 Dihedral : 15.481 172.971 1045 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 0.89 (0.31), residues: 758 helix: 2.20 (0.34), residues: 227 sheet: 0.51 (0.37), residues: 206 loop : -0.49 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 255 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 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6625) covalent geometry : angle 0.51399 / 0.28 ( 9073) hydrogen bonds : bond 0.03904 / 2.58 ( 261) hydrogen bonds : angle 4.43700 / 3.19 ( 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 : 0.236 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8127 (ttpt) REVERT: A 147 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 573 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8146 (mtm-85) outliers start: 12 outliers final: 5 residues processed: 65 average time/residue: 0.6142 time to fit residues: 41.9405 Evaluate side-chains 59 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 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 128 PHE Chi-restraints excluded: chain A residue 147 GLU 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 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: 0.7980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.183995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130317 restraints weight = 6750.438| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.22 r_work: 0.3183 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6625 Z= 0.159 Angle : 0.529 6.120 9073 Z= 0.282 Chirality : 0.044 0.283 997 Planarity : 0.004 0.042 1127 Dihedral : 15.475 172.131 1045 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.69 % Allowed : 15.69 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.31), residues: 758 helix: 2.19 (0.34), residues: 227 sheet: 0.51 (0.37), residues: 206 loop : -0.50 (0.33), residues: 325 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 0.012 0.001 TRP A 136 HIS 0.008 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6625) covalent geometry : angle 0.52873 / 0.28 ( 9073) hydrogen bonds : bond 0.04017 / 2.65 ( 261) hydrogen bonds : angle 4.41647 / 3.18 ( 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 64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: A 573 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8161 (mtm-85) outliers start: 11 outliers final: 5 residues processed: 61 average time/residue: 0.6111 time to fit residues: 39.1949 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 153 ASP 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 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: 2.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.0000 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.185006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131472 restraints weight = 6740.748| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.21 r_work: 0.3204 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1643 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= 0.132 Angle : 0.503 6.558 9073 Z= 0.269 Chirality : 0.043 0.281 997 Planarity : 0.004 0.040 1127 Dihedral : 15.460 170.675 1045 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.54 % Allowed : 15.85 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.96 (0.31), residues: 758 helix: 2.29 (0.34), residues: 227 sheet: 0.54 (0.37), residues: 206 loop : -0.47 (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 0.017 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 0.00303 / 0.13 ( 6625) covalent geometry : angle 0.50317 / 0.27 ( 9073) hydrogen bonds : bond 0.03611 / 2.38 ( 261) hydrogen bonds : angle 4.32466 / 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 64 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8131 (ttpt) REVERT: A 573 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8166 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 0.5253 time to fit residues: 33.8109 Evaluate side-chains 61 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 153 ASP 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 573 ARG 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: 10.0000 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.179041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127540 restraints weight = 6754.793| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.18 r_work: 0.3183 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6625 Z= 0.196 Angle : 0.569 7.123 9073 Z= 0.300 Chirality : 0.045 0.290 997 Planarity : 0.005 0.045 1127 Dihedral : 15.473 169.489 1045 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 15.23 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.30), residues: 758 helix: 2.12 (0.34), residues: 227 sheet: 0.71 (0.39), residues: 186 loop : -0.60 (0.32), residues: 345 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 0.019 0.002 PHE A 469 TRP 0.010 0.002 TRP A 136 HIS 0.010 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 6625) covalent geometry : angle 0.56855 / 0.30 ( 9073) hydrogen bonds : bond 0.04419 / 2.92 ( 261) hydrogen bonds : angle 4.43899 / 3.19 ( 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 69 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 255 ARG cc_start: 0.8224 (ttt90) cc_final: 0.8004 (ttp80) REVERT: A 573 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8134 (mtm-85) REVERT: A 698 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7543 (ttp80) outliers start: 14 outliers final: 4 residues processed: 66 average time/residue: 0.5994 time to fit residues: 41.5062 Evaluate side-chains 56 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 573 ARG 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: 7.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 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 = 0.4022 r_free = 0.4022 target = 0.179164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127327 restraints weight = 6751.138| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.08 r_work: 0.3185 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6625 Z= 0.199 Angle : 0.574 7.381 9073 Z= 0.302 Chirality : 0.045 0.288 997 Planarity : 0.005 0.044 1127 Dihedral : 15.502 168.282 1045 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 16.15 % Favored : 82.77 % 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: 0.75 (0.30), residues: 758 helix: 2.03 (0.34), residues: 227 sheet: 0.68 (0.39), residues: 186 loop : -0.64 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 157 TYR 0.018 0.002 TYR A 377 PHE 0.018 0.002 PHE A 469 TRP 0.011 0.002 TRP A 136 HIS 0.010 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 6625) covalent geometry : angle 0.57415 / 0.30 ( 9073) hydrogen bonds : bond 0.04445 / 2.93 ( 261) hydrogen bonds : angle 4.47404 / 3.21 ( 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 58 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.222 Fit side-chains REVERT: A 573 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8155 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.6152 time to fit residues: 36.1519 Evaluate side-chains 54 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 573 ARG Chi-restraints excluded: chain A residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 67 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 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 = 0.4103 r_free = 0.4103 target = 0.186584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133712 restraints weight = 6722.479| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.18 r_work: 0.3232 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1689 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= 0.105 Angle : 0.485 7.175 9073 Z= 0.261 Chirality : 0.042 0.274 997 Planarity : 0.004 0.039 1127 Dihedral : 15.486 166.058 1045 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.46 % Allowed : 16.77 % Favored : 82.77 % 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: 1.03 (0.31), residues: 758 helix: 2.30 (0.34), residues: 227 sheet: 0.81 (0.39), residues: 186 loop : -0.49 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 157 TYR 0.010 0.001 TYR A 377 PHE 0.017 0.001 PHE A 469 TRP 0.016 0.001 TRP A 570 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 6625) covalent geometry : angle 0.48517 / 0.26 ( 9073) hydrogen bonds : bond 0.03093 / 2.03 ( 261) hydrogen bonds : angle 4.21749 / 3.03 ( 795) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1789.10 seconds wall clock time: 31 minutes 16.66 seconds (1876.66 seconds total)