Starting phenix.real_space_refine on Wed Sep 17 03:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3c_44134/09_2025/9b3c_44134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3c_44134/09_2025/9b3c_44134.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/9b3c_44134/09_2025/9b3c_44134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3c_44134/09_2025/9b3c_44134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3c_44134/09_2025/9b3c_44134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3c_44134/09_2025/9b3c_44134.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= 0.002 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2130 2.51 5 N 540 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 53 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: G, M, S, C, I, O, U, E, K, Q, W, Y, a, c, H, N, T, D, J, P, V, F, L, R, X, Z, b, d Time building chain proxies: 0.48, per 1000 atoms: 0.15 Number of scatterers: 3270 At special positions: 0 Unit cell: (75.624, 79.734, 42.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 570 8.00 N 540 7.00 C 2130 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=45, symmetry=0 Number of additional bonds: simple=45, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 100.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 310 removed outlier: 6.612A pdb=" N SER A 305 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE G 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR G 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 309 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER G 305 " --> pdb=" O VAL M 306 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE M 308 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN G 307 " --> pdb=" O ILE M 308 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N TYR M 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL G 309 " --> pdb=" O TYR M 310 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER M 305 " --> pdb=" O VAL S 306 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE S 308 " --> pdb=" O SER M 305 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN M 307 " --> pdb=" O ILE S 308 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR S 310 " --> pdb=" O GLN M 307 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL M 309 " --> pdb=" O TYR S 310 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER S 305 " --> pdb=" O VAL Y 306 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE Y 308 " --> pdb=" O SER S 305 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLN S 307 " --> pdb=" O ILE Y 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR Y 310 " --> pdb=" O GLN S 307 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL S 309 " --> pdb=" O TYR Y 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 306 through 309 Processing sheet with id=AA4, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AA5, first strand: chain 'C' and resid 305 through 310 removed outlier: 6.616A pdb=" N SER C 305 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE I 308 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN C 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR I 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER I 305 " --> pdb=" O VAL O 306 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE O 308 " --> pdb=" O SER I 305 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN I 307 " --> pdb=" O ILE O 308 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR O 310 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL I 309 " --> pdb=" O TYR O 310 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER O 305 " --> pdb=" O VAL U 306 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE U 308 " --> pdb=" O SER O 305 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN O 307 " --> pdb=" O ILE U 308 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR U 310 " --> pdb=" O GLN O 307 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL O 309 " --> pdb=" O TYR U 310 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER U 305 " --> pdb=" O VAL a 306 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE a 308 " --> pdb=" O SER U 305 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN U 307 " --> pdb=" O ILE a 308 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR a 310 " --> pdb=" O GLN U 307 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL U 309 " --> pdb=" O TYR a 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 306 through 309 Processing sheet with id=AA7, first strand: chain 'E' and resid 298 through 299 Processing sheet with id=AA8, first strand: chain 'E' and resid 305 through 310 removed outlier: 6.628A pdb=" N SER E 305 " --> pdb=" O VAL K 306 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE K 308 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN E 307 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR K 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL E 309 " --> pdb=" O TYR K 310 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER K 305 " --> pdb=" O VAL Q 306 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE Q 308 " --> pdb=" O SER K 305 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN K 307 " --> pdb=" O ILE Q 308 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR Q 310 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL K 309 " --> pdb=" O TYR Q 310 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER Q 305 " --> pdb=" O VAL W 306 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE W 308 " --> pdb=" O SER Q 305 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN Q 307 " --> pdb=" O ILE W 308 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR W 310 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL Q 309 " --> pdb=" O TYR W 310 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER W 305 " --> pdb=" O VAL c 306 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE c 308 " --> pdb=" O SER W 305 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN W 307 " --> pdb=" O ILE c 308 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR c 310 " --> pdb=" O GLN W 307 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL W 309 " --> pdb=" O TYR c 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 306 through 309 48 hydrogen bonds defined for protein. 144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.31 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: 990 1.34 - 1.45: 507 1.45 - 1.57: 1773 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 3300 Sorted by residual: bond pdb=" CA LYS c 311 " pdb=" C LYS c 311 " ideal model delta sigma weight residual 1.534 1.520 0.014 9.50e-03 1.11e+04 2.32e+00 bond pdb=" CA LYS a 311 " pdb=" C LYS a 311 " ideal model delta sigma weight residual 1.534 1.520 0.014 9.50e-03 1.11e+04 2.25e+00 bond pdb=" CA LYS K 311 " pdb=" C LYS K 311 " ideal model delta sigma weight residual 1.534 1.520 0.014 9.50e-03 1.11e+04 2.14e+00 bond pdb=" CA LYS Y 311 " pdb=" C LYS Y 311 " ideal model delta sigma weight residual 1.534 1.520 0.014 9.50e-03 1.11e+04 2.14e+00 bond pdb=" CA LYS C 311 " pdb=" C LYS C 311 " ideal model delta sigma weight residual 1.534 1.520 0.014 9.50e-03 1.11e+04 2.13e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.76: 3778 0.76 - 1.52: 498 1.52 - 2.28: 59 2.28 - 3.04: 90 3.04 - 3.80: 15 Bond angle restraints: 4440 Sorted by residual: angle pdb=" C LYS S 311 " pdb=" CA LYS S 311 " pdb=" CB LYS S 311 " ideal model delta sigma weight residual 111.20 108.70 2.50 7.10e-01 1.98e+00 1.24e+01 angle pdb=" C LYS K 311 " pdb=" CA LYS K 311 " pdb=" CB LYS K 311 " ideal model delta sigma weight residual 111.20 108.72 2.48 7.10e-01 1.98e+00 1.22e+01 angle pdb=" C LYS Q 311 " pdb=" CA LYS Q 311 " pdb=" CB LYS Q 311 " ideal model delta sigma weight residual 111.20 108.73 2.47 7.10e-01 1.98e+00 1.21e+01 angle pdb=" C LYS G 311 " pdb=" CA LYS G 311 " pdb=" CB LYS G 311 " ideal model delta sigma weight residual 111.20 108.74 2.46 7.10e-01 1.98e+00 1.21e+01 angle pdb=" C LYS c 311 " pdb=" CA LYS c 311 " pdb=" CB LYS c 311 " ideal model delta sigma weight residual 111.20 108.75 2.45 7.10e-01 1.98e+00 1.19e+01 ... (remaining 4435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.56: 1635 8.56 - 17.11: 150 17.11 - 25.67: 30 25.67 - 34.23: 0 34.23 - 42.79: 45 Dihedral angle restraints: 1860 sinusoidal: 720 harmonic: 1140 Sorted by residual: dihedral pdb=" CA ASP G 295 " pdb=" CB ASP G 295 " pdb=" CG ASP G 295 " pdb=" OD1 ASP G 295 " ideal model delta sinusoidal sigma weight residual -30.00 -71.79 41.79 1 2.00e+01 2.50e-03 6.11e+00 dihedral pdb=" CA ASP W 295 " pdb=" CB ASP W 295 " pdb=" CG ASP W 295 " pdb=" OD1 ASP W 295 " ideal model delta sinusoidal sigma weight residual -30.00 -71.79 41.79 1 2.00e+01 2.50e-03 6.10e+00 dihedral pdb=" CA ASP Q 295 " pdb=" CB ASP Q 295 " pdb=" CG ASP Q 295 " pdb=" OD1 ASP Q 295 " ideal model delta sinusoidal sigma weight residual -30.00 -71.75 41.75 1 2.00e+01 2.50e-03 6.10e+00 ... (remaining 1857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 234 0.028 - 0.056: 52 0.056 - 0.084: 44 0.084 - 0.111: 113 0.111 - 0.139: 52 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA ILE R 308 " pdb=" N ILE R 308 " pdb=" C ILE R 308 " pdb=" CB ILE R 308 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE J 308 " pdb=" N ILE J 308 " pdb=" C ILE J 308 " pdb=" CB ILE J 308 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE H 308 " pdb=" N ILE H 308 " pdb=" C ILE H 308 " pdb=" CB ILE H 308 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 492 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL Q 300 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO Q 301 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO Q 301 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO Q 301 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL W 300 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO W 301 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO W 301 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO W 301 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL O 300 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO O 301 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO O 301 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO O 301 " 0.021 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1139 2.87 - 3.38: 2645 3.38 - 3.89: 6026 3.89 - 4.39: 5846 4.39 - 4.90: 12651 Nonbonded interactions: 28307 Sorted by model distance: nonbonded pdb=" NZ LYS I 311 " pdb=" OD1 ASP Q 295 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS C 311 " pdb=" OD1 ASP K 295 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS O 311 " pdb=" OD1 ASP W 295 " model vdw 2.369 3.120 nonbonded pdb=" NZ LYS U 311 " pdb=" OD1 ASP c 295 " model vdw 2.373 3.120 nonbonded pdb=" CB CYS I 314 " pdb=" N NH2 I 401 " model vdw 2.547 2.816 ... (remaining 28302 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'M' selection = chain 'S' selection = chain 'C' selection = chain 'I' selection = chain 'O' selection = chain 'U' selection = chain 'E' selection = chain 'K' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'N' selection = chain 'T' selection = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'V' selection = chain 'F' selection = chain 'L' selection = chain 'R' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' } 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: 2.370 Set stop_for_unknowns flag: 0.010 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.008 0.043 3345 Z= 0.312 Angle : 0.636 3.798 4440 Z= 0.397 Chirality : 0.068 0.139 495 Planarity : 0.007 0.037 555 Dihedral : 10.579 42.785 1140 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 0.24 (0.46), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.19 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR X 310 HIS 0.003 0.002 HIS U 299 Details of bonding type rmsd covalent geometry : bond 0.00791 ( 3300) covalent geometry : angle 0.63590 ( 4440) hydrogen bonds : bond 0.03605 ( 48) hydrogen bonds : angle 6.20990 ( 144) Misc. bond : bond 0.00141 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4363 time to fit residues: 41.0758 Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 307 GLN C 296 ASN Q 299 HIS Z 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.144867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124460 restraints weight = 4016.461| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.77 r_work: 0.3640 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3345 Z= 0.124 Angle : 0.495 3.768 4440 Z= 0.252 Chirality : 0.069 0.147 495 Planarity : 0.005 0.037 555 Dihedral : 7.719 42.809 450 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.06 % Allowed : 11.94 % Favored : 85.00 % 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 aren not related in a simple way. whole: -0.03 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.01 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR V 310 HIS 0.003 0.001 HIS S 299 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3300) covalent geometry : angle 0.49533 ( 4440) hydrogen bonds : bond 0.01629 ( 48) hydrogen bonds : angle 5.52162 ( 144) Misc. bond : bond 0.00038 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.207 Fit side-chains REVERT: M 298 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8097 (tptp) REVERT: U 298 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7517 (mppt) REVERT: R 307 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: R 310 TYR cc_start: 0.4774 (m-80) cc_final: 0.3972 (t80) REVERT: X 310 TYR cc_start: 0.4664 (m-80) cc_final: 0.4045 (t80) REVERT: a 298 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7817 (mmmt) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.3680 time to fit residues: 33.6892 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain R residue 307 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN W 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.122537 restraints weight = 3946.690| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.82 r_work: 0.3549 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3345 Z= 0.163 Angle : 0.557 4.833 4440 Z= 0.284 Chirality : 0.068 0.167 495 Planarity : 0.005 0.042 555 Dihedral : 7.911 52.122 450 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.44 % Allowed : 11.67 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.01 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR U 310 HIS 0.004 0.001 HIS O 299 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 3300) covalent geometry : angle 0.55694 ( 4440) hydrogen bonds : bond 0.01278 ( 48) hydrogen bonds : angle 5.06823 ( 144) Misc. bond : bond 0.00060 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.145 Fit side-chains REVERT: M 298 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8138 (tptp) REVERT: U 298 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7625 (mppt) REVERT: L 310 TYR cc_start: 0.4918 (m-80) cc_final: 0.4503 (t80) REVERT: R 307 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: R 310 TYR cc_start: 0.4706 (m-80) cc_final: 0.3909 (t80) REVERT: X 310 TYR cc_start: 0.4592 (m-80) cc_final: 0.4063 (t80) REVERT: a 298 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7806 (mmmt) REVERT: c 298 LYS cc_start: 0.7791 (tptp) cc_final: 0.7545 (tptt) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.3748 time to fit residues: 33.5666 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain R residue 307 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain c residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 299 HIS W 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123435 restraints weight = 3966.378| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.84 r_work: 0.3602 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3345 Z= 0.163 Angle : 0.547 5.849 4440 Z= 0.274 Chirality : 0.069 0.273 495 Planarity : 0.005 0.039 555 Dihedral : 8.120 57.517 450 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.06 % Allowed : 13.06 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR I 310 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3300) covalent geometry : angle 0.54652 ( 4440) hydrogen bonds : bond 0.01418 ( 48) hydrogen bonds : angle 4.80327 ( 144) Misc. bond : bond 0.00065 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.139 Fit side-chains REVERT: A 298 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8396 (ttpp) REVERT: M 298 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8175 (tptp) REVERT: U 298 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7713 (mppt) REVERT: J 305 SER cc_start: 0.8431 (p) cc_final: 0.8176 (p) REVERT: R 310 TYR cc_start: 0.4702 (m-80) cc_final: 0.3825 (t80) REVERT: X 307 GLN cc_start: 0.8008 (mt0) cc_final: 0.7790 (mt0) REVERT: X 310 TYR cc_start: 0.4546 (m-80) cc_final: 0.4029 (t80) REVERT: a 298 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7852 (mmmt) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.4304 time to fit residues: 32.5094 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125302 restraints weight = 3878.517| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.81 r_work: 0.3628 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3345 Z= 0.139 Angle : 0.525 5.210 4440 Z= 0.261 Chirality : 0.067 0.149 495 Planarity : 0.005 0.038 555 Dihedral : 8.028 59.607 450 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 15.28 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.11 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR I 310 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3300) covalent geometry : angle 0.52465 ( 4440) hydrogen bonds : bond 0.01434 ( 48) hydrogen bonds : angle 4.73083 ( 144) Misc. bond : bond 0.00053 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.138 Fit side-chains REVERT: A 298 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (ttpp) REVERT: M 298 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8121 (tptp) REVERT: B 310 TYR cc_start: 0.5902 (m-80) cc_final: 0.5651 (m-80) REVERT: I 298 LYS cc_start: 0.8327 (mppt) cc_final: 0.7969 (mtpt) REVERT: U 298 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7528 (mppt) REVERT: J 305 SER cc_start: 0.8439 (p) cc_final: 0.8183 (p) REVERT: R 310 TYR cc_start: 0.4752 (m-80) cc_final: 0.3849 (t80) REVERT: X 310 TYR cc_start: 0.4626 (m-80) cc_final: 0.4058 (t80) REVERT: a 298 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7786 (mppt) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.4382 time to fit residues: 33.6129 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122009 restraints weight = 3919.936| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.79 r_work: 0.3593 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3345 Z= 0.175 Angle : 0.558 5.305 4440 Z= 0.277 Chirality : 0.068 0.158 495 Planarity : 0.005 0.039 555 Dihedral : 8.207 56.612 450 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.33 % Allowed : 15.56 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR I 310 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3300) covalent geometry : angle 0.55792 ( 4440) hydrogen bonds : bond 0.01424 ( 48) hydrogen bonds : angle 4.58408 ( 144) Misc. bond : bond 0.00068 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.100 Fit side-chains REVERT: A 298 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8435 (ttpp) REVERT: M 298 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (tptp) REVERT: U 298 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7675 (mppt) REVERT: J 305 SER cc_start: 0.8456 (p) cc_final: 0.8192 (p) REVERT: R 310 TYR cc_start: 0.4832 (m-80) cc_final: 0.3928 (t80) REVERT: X 310 TYR cc_start: 0.4600 (m-80) cc_final: 0.4095 (t80) REVERT: a 298 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7874 (mmmt) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.4134 time to fit residues: 34.3040 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.146808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125842 restraints weight = 3969.248| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.76 r_work: 0.3628 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3345 Z= 0.103 Angle : 0.488 4.946 4440 Z= 0.242 Chirality : 0.067 0.157 495 Planarity : 0.005 0.038 555 Dihedral : 7.818 56.336 450 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 17.22 % Favored : 80.00 % 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 aren not related in a simple way. whole: -0.04 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.02 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR I 310 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3300) covalent geometry : angle 0.48779 ( 4440) hydrogen bonds : bond 0.01527 ( 48) hydrogen bonds : angle 4.62265 ( 144) Misc. bond : bond 0.00030 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.162 Fit side-chains REVERT: A 298 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8118 (tttp) REVERT: M 298 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8057 (tptp) REVERT: U 298 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7600 (mppt) REVERT: J 305 SER cc_start: 0.8395 (p) cc_final: 0.8132 (p) REVERT: X 310 TYR cc_start: 0.4562 (m-80) cc_final: 0.4083 (t80) REVERT: a 298 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7735 (mmmt) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.4062 time to fit residues: 31.5709 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 0.0030 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.140054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.117737 restraints weight = 4119.603| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.82 r_work: 0.3545 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3345 Z= 0.258 Angle : 0.614 5.768 4440 Z= 0.305 Chirality : 0.070 0.157 495 Planarity : 0.005 0.039 555 Dihedral : 8.440 57.708 450 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 18.33 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.002 TYR I 310 HIS 0.004 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00669 ( 3300) covalent geometry : angle 0.61363 ( 4440) hydrogen bonds : bond 0.01447 ( 48) hydrogen bonds : angle 4.61948 ( 144) Misc. bond : bond 0.00108 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.138 Fit side-chains REVERT: A 298 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8300 (tttp) REVERT: M 298 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8291 (tptp) REVERT: U 298 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7801 (mtpt) REVERT: J 305 SER cc_start: 0.8460 (p) cc_final: 0.8193 (p) REVERT: X 310 TYR cc_start: 0.4621 (m-80) cc_final: 0.4142 (t80) REVERT: a 298 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7924 (mmmt) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.4107 time to fit residues: 33.2215 Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain W residue 305 SER Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.0020 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.146757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125501 restraints weight = 3993.600| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.78 r_work: 0.3619 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3345 Z= 0.102 Angle : 0.495 5.412 4440 Z= 0.245 Chirality : 0.068 0.158 495 Planarity : 0.005 0.038 555 Dihedral : 7.951 53.875 450 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 19.44 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.00 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.001 TYR I 310 HIS 0.004 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3300) covalent geometry : angle 0.49508 ( 4440) hydrogen bonds : bond 0.01474 ( 48) hydrogen bonds : angle 4.59479 ( 144) Misc. bond : bond 0.00042 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.142 Fit side-chains REVERT: A 298 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8121 (tttp) REVERT: M 298 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (tptp) REVERT: U 298 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7604 (mppt) REVERT: J 305 SER cc_start: 0.8386 (p) cc_final: 0.8122 (p) REVERT: X 310 TYR cc_start: 0.4598 (m-80) cc_final: 0.4022 (t80) REVERT: a 298 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7699 (mmmt) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 0.3836 time to fit residues: 29.1418 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130399 restraints weight = 3949.281| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.77 r_work: 0.3688 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3345 Z= 0.099 Angle : 0.484 5.674 4440 Z= 0.240 Chirality : 0.067 0.166 495 Planarity : 0.005 0.038 555 Dihedral : 7.628 53.240 450 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 20.28 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.03 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.001 TYR I 310 HIS 0.004 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3300) covalent geometry : angle 0.48423 ( 4440) hydrogen bonds : bond 0.01440 ( 48) hydrogen bonds : angle 4.66440 ( 144) Misc. bond : bond 0.00026 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.088 Fit side-chains REVERT: A 298 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7983 (tttp) REVERT: U 298 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7558 (mtpt) REVERT: J 305 SER cc_start: 0.8388 (p) cc_final: 0.8127 (p) REVERT: X 310 TYR cc_start: 0.4499 (m-80) cc_final: 0.4031 (t80) REVERT: a 298 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7703 (mmmt) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.3543 time to fit residues: 28.8468 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 300 VAL Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.149257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.128309 restraints weight = 4020.073| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.77 r_work: 0.3690 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3345 Z= 0.127 Angle : 0.511 5.780 4440 Z= 0.252 Chirality : 0.067 0.175 495 Planarity : 0.005 0.038 555 Dihedral : 7.573 52.746 450 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.94 % Allowed : 20.56 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.46), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.12 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.001 TYR U 310 HIS 0.004 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3300) covalent geometry : angle 0.51131 ( 4440) hydrogen bonds : bond 0.01448 ( 48) hydrogen bonds : angle 4.67489 ( 144) Misc. bond : bond 0.00041 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.87 seconds wall clock time: 24 minutes 20.67 seconds (1460.67 seconds total)