Starting phenix.real_space_refine on Sat Apr 26 19:56:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3c_44134/04_2025/9b3c_44134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3c_44134/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3c_44134/04_2025/9b3c_44134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3c_44134/04_2025/9b3c_44134.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3c_44134/04_2025/9b3c_44134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3c_44134/04_2025/9b3c_44134.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, D, F, H, J, L, N, P, R, T, V, X, Z, b, d Time building chain proxies: 1.74, per 1000 atoms: 0.53 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: 1.00 Conformation dependent library (CDL) restraints added in 322.0 milliseconds 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: 0.44 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: 0.69 Time building geometry restraints manager: 1.04 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- 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 : 3.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (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 HIS 0.003 0.002 HIS U 299 TYR 0.014 0.002 TYR X 310 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 48) hydrogen bonds : angle 6.20990 ( 144) covalent geometry : bond 0.00791 ( 3300) covalent geometry : angle 0.63590 ( 4440) 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 : 0.357 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.8571 time to fit residues: 80.9075 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.144000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.123353 restraints weight = 3978.243| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.78 r_work: 0.3642 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1944 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= 0.122 Angle : 0.499 3.779 4440 Z= 0.254 Chirality : 0.069 0.154 495 Planarity : 0.005 0.038 555 Dihedral : 7.775 43.541 450 Min Nonbonded Distance : 2.621 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 HIS 0.003 0.001 HIS S 299 TYR 0.010 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01503 ( 48) hydrogen bonds : angle 5.43670 ( 144) covalent geometry : bond 0.00307 ( 3300) covalent geometry : angle 0.49907 ( 4440) Misc. bond : bond 0.00037 ( 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 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.398 Fit side-chains REVERT: M 298 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (tptp) REVERT: U 298 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7529 (mppt) REVERT: R 307 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: R 310 TYR cc_start: 0.4774 (m-80) cc_final: 0.3908 (t80) REVERT: X 310 TYR cc_start: 0.4639 (m-80) cc_final: 0.4026 (t80) REVERT: a 298 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7815 (mmmt) outliers start: 11 outliers final: 2 residues processed: 86 average time/residue: 0.8010 time to fit residues: 71.7610 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 27 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.0570 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124440 restraints weight = 3886.740| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.82 r_work: 0.3672 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3345 Z= 0.126 Angle : 0.522 5.340 4440 Z= 0.266 Chirality : 0.067 0.145 495 Planarity : 0.005 0.042 555 Dihedral : 7.552 47.204 450 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.61 % Allowed : 13.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.45), 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 HIS 0.004 0.001 HIS O 299 TYR 0.010 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01359 ( 48) hydrogen bonds : angle 5.13423 ( 144) covalent geometry : bond 0.00324 ( 3300) covalent geometry : angle 0.52207 ( 4440) Misc. bond : bond 0.00041 ( 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 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.392 Fit side-chains REVERT: M 298 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8118 (tptp) REVERT: L 310 TYR cc_start: 0.4862 (m-80) cc_final: 0.4480 (t80) REVERT: R 307 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: R 310 TYR cc_start: 0.4694 (m-80) cc_final: 0.3935 (t80) REVERT: X 310 TYR cc_start: 0.4595 (m-80) cc_final: 0.4026 (t80) REVERT: a 298 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7797 (mmmt) outliers start: 13 outliers final: 8 residues processed: 83 average time/residue: 0.7772 time to fit residues: 67.2671 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain O 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 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 299 HIS K 299 HIS W 296 ASN W 299 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121396 restraints weight = 3954.941| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.84 r_work: 0.3603 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3345 Z= 0.181 Angle : 0.560 6.158 4440 Z= 0.281 Chirality : 0.069 0.259 495 Planarity : 0.005 0.039 555 Dihedral : 8.106 57.314 450 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.06 % Allowed : 13.33 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.04 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 299 TYR 0.011 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01373 ( 48) hydrogen bonds : angle 4.79321 ( 144) covalent geometry : bond 0.00475 ( 3300) covalent geometry : angle 0.56047 ( 4440) Misc. bond : bond 0.00077 ( 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 : 0.382 Fit side-chains REVERT: A 298 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (ttpp) REVERT: M 298 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8203 (tptp) REVERT: B 310 TYR cc_start: 0.5924 (m-80) cc_final: 0.5370 (m-80) REVERT: U 298 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7781 (mppt) REVERT: J 305 SER cc_start: 0.8535 (p) cc_final: 0.8304 (p) REVERT: R 310 TYR cc_start: 0.4715 (m-80) cc_final: 0.3865 (t80) REVERT: X 307 GLN cc_start: 0.8050 (mt0) cc_final: 0.7821 (mt0) REVERT: X 310 TYR cc_start: 0.4554 (m-80) cc_final: 0.4032 (t80) REVERT: a 298 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7869 (mmmt) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.8978 time to fit residues: 68.0622 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 0.0980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.147288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126780 restraints weight = 3931.841| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.80 r_work: 0.3686 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3037 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= 0.098 Angle : 0.488 5.018 4440 Z= 0.243 Chirality : 0.067 0.139 495 Planarity : 0.005 0.037 555 Dihedral : 7.684 57.503 450 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 14.44 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 299 TYR 0.009 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01368 ( 48) hydrogen bonds : angle 4.71138 ( 144) covalent geometry : bond 0.00246 ( 3300) covalent geometry : angle 0.48815 ( 4440) Misc. bond : bond 0.00021 ( 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 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.349 Fit side-chains REVERT: A 298 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7999 (tttp) REVERT: M 298 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8038 (tptp) REVERT: U 298 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7601 (mppt) REVERT: J 305 SER cc_start: 0.8415 (p) cc_final: 0.8173 (p) REVERT: R 310 TYR cc_start: 0.4740 (m-80) cc_final: 0.3862 (t80) REVERT: X 310 TYR cc_start: 0.4554 (m-80) cc_final: 0.4019 (t80) REVERT: a 298 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7796 (mmmt) outliers start: 10 outliers final: 3 residues processed: 71 average time/residue: 0.8078 time to fit residues: 59.7039 Evaluate side-chains 75 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.145926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124531 restraints weight = 4076.256| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.86 r_work: 0.3641 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3345 Z= 0.137 Angle : 0.520 4.928 4440 Z= 0.258 Chirality : 0.067 0.154 495 Planarity : 0.005 0.037 555 Dihedral : 7.846 59.770 450 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 16.67 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 HIS 0.003 0.001 HIS C 299 TYR 0.012 0.001 TYR I 310 Details of bonding type rmsd hydrogen bonds : bond 0.01550 ( 48) hydrogen bonds : angle 4.72023 ( 144) covalent geometry : bond 0.00359 ( 3300) covalent geometry : angle 0.51985 ( 4440) Misc. bond : bond 0.00044 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.377 Fit side-chains REVERT: M 298 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8164 (tptp) REVERT: I 298 LYS cc_start: 0.8329 (mppt) cc_final: 0.8002 (mtpp) REVERT: U 298 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7708 (mppt) REVERT: J 305 SER cc_start: 0.8440 (p) cc_final: 0.8190 (p) REVERT: R 310 TYR cc_start: 0.4808 (m-80) cc_final: 0.3909 (t80) REVERT: X 310 TYR cc_start: 0.4568 (m-80) cc_final: 0.4098 (t80) REVERT: a 298 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7877 (mmmt) outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.8335 time to fit residues: 65.0134 Evaluate side-chains 77 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.147906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.126793 restraints weight = 3919.719| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.81 r_work: 0.3672 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3316 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= 0.111 Angle : 0.491 5.184 4440 Z= 0.243 Chirality : 0.067 0.158 495 Planarity : 0.005 0.037 555 Dihedral : 7.725 59.200 450 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.50 % Allowed : 16.67 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.45), 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 HIS 0.003 0.001 HIS C 299 TYR 0.014 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01363 ( 48) hydrogen bonds : angle 4.60581 ( 144) covalent geometry : bond 0.00285 ( 3300) covalent geometry : angle 0.49110 ( 4440) Misc. bond : bond 0.00035 ( 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.341 Fit side-chains REVERT: M 298 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8141 (tptp) REVERT: U 298 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7697 (mppt) REVERT: J 305 SER cc_start: 0.8436 (p) cc_final: 0.8190 (p) REVERT: R 310 TYR cc_start: 0.4802 (m-80) cc_final: 0.3912 (t80) REVERT: X 310 TYR cc_start: 0.4537 (m-80) cc_final: 0.4158 (t80) REVERT: a 298 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7853 (mmmt) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.8445 time to fit residues: 67.5502 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.0050 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 overall best weight: 0.3530 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.152824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.132821 restraints weight = 3888.821| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.78 r_work: 0.3714 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3345 Z= 0.083 Angle : 0.463 5.299 4440 Z= 0.229 Chirality : 0.066 0.152 495 Planarity : 0.005 0.036 555 Dihedral : 7.373 59.477 450 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.50 % Allowed : 16.94 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (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 HIS 0.003 0.001 HIS I 299 TYR 0.011 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01440 ( 48) hydrogen bonds : angle 4.56162 ( 144) covalent geometry : bond 0.00206 ( 3300) covalent geometry : angle 0.46343 ( 4440) Misc. bond : bond 0.00015 ( 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: 9 poor density : 77 time to evaluate : 0.418 Fit side-chains REVERT: M 298 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8029 (tptp) REVERT: U 298 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7608 (mtpt) REVERT: J 305 SER cc_start: 0.8394 (p) cc_final: 0.8138 (p) REVERT: K 298 LYS cc_start: 0.8137 (tptm) cc_final: 0.7901 (tppt) REVERT: X 310 TYR cc_start: 0.4548 (m-80) cc_final: 0.4138 (t80) outliers start: 9 outliers final: 4 residues processed: 79 average time/residue: 0.8957 time to fit residues: 73.4694 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 U residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.151031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130693 restraints weight = 3903.309| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.79 r_work: 0.3697 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3345 Z= 0.103 Angle : 0.487 5.757 4440 Z= 0.241 Chirality : 0.066 0.159 495 Planarity : 0.004 0.035 555 Dihedral : 7.358 59.155 450 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 1.67 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.07 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.021 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01365 ( 48) hydrogen bonds : angle 4.50306 ( 144) covalent geometry : bond 0.00264 ( 3300) covalent geometry : angle 0.48655 ( 4440) Misc. bond : bond 0.00029 ( 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: 6 poor density : 74 time to evaluate : 0.391 Fit side-chains REVERT: M 298 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8124 (tptp) REVERT: U 298 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: J 305 SER cc_start: 0.8425 (p) cc_final: 0.8171 (p) REVERT: K 298 LYS cc_start: 0.8204 (tptm) cc_final: 0.7972 (tppt) REVERT: X 310 TYR cc_start: 0.4610 (m-80) cc_final: 0.4084 (t80) REVERT: a 298 LYS cc_start: 0.8261 (tppt) cc_final: 0.7815 (mmmt) outliers start: 6 outliers final: 4 residues processed: 75 average time/residue: 0.8485 time to fit residues: 66.1067 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 U residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.150139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129481 restraints weight = 3839.939| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.77 r_work: 0.3727 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3345 Z= 0.111 Angle : 0.493 5.825 4440 Z= 0.245 Chirality : 0.066 0.160 495 Planarity : 0.004 0.035 555 Dihedral : 7.412 58.277 450 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 19.17 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 299 TYR 0.024 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01434 ( 48) hydrogen bonds : angle 4.50965 ( 144) covalent geometry : bond 0.00281 ( 3300) covalent geometry : angle 0.49327 ( 4440) Misc. bond : bond 0.00034 ( 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 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.392 Fit side-chains REVERT: M 298 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (tptp) REVERT: U 298 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7734 (mtpt) REVERT: J 305 SER cc_start: 0.8463 (p) cc_final: 0.8221 (p) REVERT: K 298 LYS cc_start: 0.8251 (tptm) cc_final: 0.8038 (tppt) REVERT: X 310 TYR cc_start: 0.4627 (m-80) cc_final: 0.4115 (t80) REVERT: a 298 LYS cc_start: 0.8331 (tppt) cc_final: 0.7894 (mmmt) outliers start: 6 outliers final: 4 residues processed: 77 average time/residue: 0.8095 time to fit residues: 64.8956 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 : 0.379 ------------------------------------------------------------------------------- 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 U residue 298 LYS Chi-restraints excluded: chain c residue 300 VAL Chi-restraints excluded: chain d residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.152664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132228 restraints weight = 3905.421| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.79 r_work: 0.3753 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3345 Z= 0.098 Angle : 0.480 5.782 4440 Z= 0.238 Chirality : 0.066 0.159 495 Planarity : 0.004 0.035 555 Dihedral : 7.287 57.905 450 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.94 % Allowed : 18.61 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.46), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.027 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01356 ( 48) hydrogen bonds : angle 4.47761 ( 144) covalent geometry : bond 0.00247 ( 3300) covalent geometry : angle 0.48042 ( 4440) Misc. bond : bond 0.00026 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2805.78 seconds wall clock time: 49 minutes 12.02 seconds (2952.02 seconds total)