Starting phenix.real_space_refine on Fri May 9 17:31:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3c_44134/05_2025/9b3c_44134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3c_44134/05_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_44134/05_2025/9b3c_44134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3c_44134/05_2025/9b3c_44134.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3c_44134/05_2025/9b3c_44134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3c_44134/05_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-5687/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: 1.59, per 1000 atoms: 0.49 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: 1.06 Conformation dependent library (CDL) restraints added in 370.2 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: 0.49 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: 0.78 Time building geometry restraints manager: 1.10 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.070 Find NCS groups from input model: 0.090 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- 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 : 0.305 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.8623 time to fit residues: 81.3661 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 : 0.396 ------------------------------------------------------------------------------- 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 = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123401 restraints weight = 3982.544| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.77 r_work: 0.3644 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 3.778 4440 Z= 0.254 Chirality : 0.069 0.154 495 Planarity : 0.005 0.038 555 Dihedral : 7.775 43.542 450 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 5.43667 ( 144) covalent geometry : bond 0.00307 ( 3300) covalent geometry : angle 0.49903 ( 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 : 0.390 Fit side-chains REVERT: M 298 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8093 (tptp) REVERT: U 298 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7529 (mppt) REVERT: R 307 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: R 310 TYR cc_start: 0.4787 (m-80) cc_final: 0.3918 (t80) REVERT: X 310 TYR cc_start: 0.4651 (m-80) cc_final: 0.4035 (t80) REVERT: a 298 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7818 (mmmt) outliers start: 11 outliers final: 2 residues processed: 86 average time/residue: 0.8343 time to fit residues: 74.6451 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 : 0.409 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.151102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130478 restraints weight = 3789.918| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.79 r_work: 0.3626 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3345 Z= 0.118 Angle : 0.517 5.423 4440 Z= 0.263 Chirality : 0.068 0.157 495 Planarity : 0.005 0.040 555 Dihedral : 7.426 46.097 450 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.06 % Allowed : 13.61 % 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: -0.06 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.03 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 299 TYR 0.009 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01430 ( 48) hydrogen bonds : angle 5.11769 ( 144) covalent geometry : bond 0.00288 ( 3300) covalent geometry : angle 0.51695 ( 4440) Misc. bond : bond 0.00033 ( 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 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.421 Fit side-chains REVERT: M 298 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8073 (tptp) REVERT: L 310 TYR cc_start: 0.4939 (m-80) cc_final: 0.4555 (t80) REVERT: R 307 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: R 310 TYR cc_start: 0.4727 (m-80) cc_final: 0.3972 (t80) REVERT: X 310 TYR cc_start: 0.4627 (m-80) cc_final: 0.4051 (t80) REVERT: a 298 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7745 (mmmt) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.7862 time to fit residues: 68.8812 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G 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 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: 0.5980 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 299 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.147329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.125715 restraints weight = 3832.726| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.77 r_work: 0.3651 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2835 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= 0.145 Angle : 0.528 5.720 4440 Z= 0.264 Chirality : 0.068 0.160 495 Planarity : 0.005 0.037 555 Dihedral : 7.810 54.179 450 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.06 % Allowed : 13.61 % 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: 0.06 (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 0.002 0.001 HIS Y 299 TYR 0.011 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01346 ( 48) hydrogen bonds : angle 4.80686 ( 144) covalent geometry : bond 0.00382 ( 3300) covalent geometry : angle 0.52811 ( 4440) Misc. bond : bond 0.00049 ( 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 : 0.368 Fit side-chains REVERT: A 298 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8035 (tttp) REVERT: M 298 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8160 (tptp) REVERT: B 310 TYR cc_start: 0.5938 (m-80) cc_final: 0.5390 (m-80) REVERT: U 298 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7618 (mppt) REVERT: J 305 SER cc_start: 0.8540 (p) cc_final: 0.8314 (p) REVERT: R 310 TYR cc_start: 0.4688 (m-80) cc_final: 0.3841 (t80) REVERT: X 310 TYR cc_start: 0.4603 (m-80) cc_final: 0.4104 (t80) REVERT: a 298 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7833 (mmmt) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.8317 time to fit residues: 63.2348 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 : 0.398 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.148150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.127402 restraints weight = 3950.351| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.85 r_work: 0.3681 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3345 Z= 0.105 Angle : 0.488 4.805 4440 Z= 0.242 Chirality : 0.067 0.148 495 Planarity : 0.005 0.036 555 Dihedral : 7.581 55.289 450 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 14.72 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 299 TYR 0.010 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01387 ( 48) hydrogen bonds : angle 4.73870 ( 144) covalent geometry : bond 0.00270 ( 3300) covalent geometry : angle 0.48785 ( 4440) Misc. bond : bond 0.00032 ( 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 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.386 Fit side-chains REVERT: A 298 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8028 (tttp) REVERT: M 298 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8094 (tptp) REVERT: U 298 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7615 (mppt) REVERT: J 305 SER cc_start: 0.8412 (p) cc_final: 0.8165 (p) REVERT: R 310 TYR cc_start: 0.4666 (m-80) cc_final: 0.3822 (t80) REVERT: X 310 TYR cc_start: 0.4502 (m-80) cc_final: 0.4045 (t80) REVERT: a 298 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7809 (mmmt) outliers start: 10 outliers final: 3 residues processed: 74 average time/residue: 0.8016 time to fit residues: 61.7610 Evaluate side-chains 74 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.149545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.128827 restraints weight = 4036.452| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.85 r_work: 0.3698 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3345 Z= 0.101 Angle : 0.478 4.571 4440 Z= 0.236 Chirality : 0.066 0.143 495 Planarity : 0.005 0.035 555 Dihedral : 7.464 55.895 450 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.29 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: -0.01 (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 HIS 0.003 0.001 HIS I 299 TYR 0.012 0.001 TYR I 310 Details of bonding type rmsd hydrogen bonds : bond 0.01357 ( 48) hydrogen bonds : angle 4.64157 ( 144) covalent geometry : bond 0.00259 ( 3300) covalent geometry : angle 0.47774 ( 4440) Misc. bond : bond 0.00028 ( 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.378 Fit side-chains REVERT: A 298 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7969 (tttp) REVERT: M 298 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8118 (tptp) REVERT: I 298 LYS cc_start: 0.8264 (mppt) cc_final: 0.7937 (mtpp) REVERT: U 298 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7634 (mppt) REVERT: J 305 SER cc_start: 0.8429 (p) cc_final: 0.8185 (p) REVERT: R 310 TYR cc_start: 0.4710 (m-80) cc_final: 0.3903 (t80) REVERT: X 310 TYR cc_start: 0.4554 (m-80) cc_final: 0.4068 (t80) REVERT: a 298 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7794 (mppt) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.7908 time to fit residues: 62.5780 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 : 0.421 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.121299 restraints weight = 3976.881| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.82 r_work: 0.3609 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3345 Z= 0.172 Angle : 0.546 5.037 4440 Z= 0.272 Chirality : 0.067 0.141 495 Planarity : 0.005 0.036 555 Dihedral : 7.996 59.371 450 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 17.50 % Favored : 79.72 % 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: 0.06 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.05 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.016 0.001 TYR I 310 Details of bonding type rmsd hydrogen bonds : bond 0.01319 ( 48) hydrogen bonds : angle 4.54105 ( 144) covalent geometry : bond 0.00449 ( 3300) covalent geometry : angle 0.54637 ( 4440) Misc. bond : bond 0.00071 ( 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 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.397 Fit side-chains REVERT: A 298 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8273 (tttp) REVERT: M 298 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8216 (tptp) REVERT: U 298 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7771 (mtpt) REVERT: J 305 SER cc_start: 0.8444 (p) cc_final: 0.8185 (p) REVERT: X 310 TYR cc_start: 0.4581 (m-80) cc_final: 0.4098 (t80) REVERT: a 298 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7891 (mmmt) outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.8647 time to fit residues: 65.5401 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 : 0.366 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.0030 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.124864 restraints weight = 3977.962| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.81 r_work: 0.3579 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3345 Z= 0.123 Angle : 0.503 5.400 4440 Z= 0.249 Chirality : 0.067 0.161 495 Planarity : 0.005 0.036 555 Dihedral : 7.793 58.261 450 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % 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: 0.02 (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 HIS 0.004 0.001 HIS I 299 TYR 0.017 0.001 TYR U 310 Details of bonding type rmsd hydrogen bonds : bond 0.01485 ( 48) hydrogen bonds : angle 4.61664 ( 144) covalent geometry : bond 0.00319 ( 3300) covalent geometry : angle 0.50262 ( 4440) Misc. bond : bond 0.00044 ( 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 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.379 Fit side-chains REVERT: A 298 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (tttp) REVERT: M 298 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8075 (tptp) REVERT: U 298 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7622 (mtpt) REVERT: J 305 SER cc_start: 0.8377 (p) cc_final: 0.8117 (p) REVERT: X 310 TYR cc_start: 0.4545 (m-80) cc_final: 0.4081 (t80) REVERT: a 298 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7762 (mmmt) outliers start: 10 outliers final: 6 residues processed: 75 average time/residue: 0.8148 time to fit residues: 63.5216 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.148113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127160 restraints weight = 3961.195| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.81 r_work: 0.3678 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3556 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= 0.115 Angle : 0.493 5.494 4440 Z= 0.244 Chirality : 0.067 0.158 495 Planarity : 0.005 0.036 555 Dihedral : 7.591 57.225 450 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % 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: 0.09 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.08 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.018 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01339 ( 48) hydrogen bonds : angle 4.53044 ( 144) covalent geometry : bond 0.00297 ( 3300) covalent geometry : angle 0.49309 ( 4440) Misc. bond : bond 0.00037 ( 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 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.393 Fit side-chains REVERT: A 298 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8225 (tttp) REVERT: M 298 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8198 (tptp) REVERT: U 298 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7744 (mtpt) REVERT: J 305 SER cc_start: 0.8434 (p) cc_final: 0.8193 (p) REVERT: X 310 TYR cc_start: 0.4602 (m-80) cc_final: 0.4067 (t80) REVERT: a 298 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7872 (mmmt) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.8062 time to fit residues: 63.7739 Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.149555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.129027 restraints weight = 3858.039| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.78 r_work: 0.3687 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3655 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 : 0.479 5.727 4440 Z= 0.237 Chirality : 0.067 0.156 495 Planarity : 0.005 0.036 555 Dihedral : 7.374 57.081 450 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.50 % Allowed : 18.06 % 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: 0.09 (0.45), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.08 (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 0.01431 ( 48) hydrogen bonds : angle 4.54346 ( 144) covalent geometry : bond 0.00251 ( 3300) covalent geometry : angle 0.47886 ( 4440) Misc. bond : bond 0.00028 ( 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 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.359 Fit side-chains REVERT: A 298 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8147 (tttp) REVERT: M 298 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8104 (tptp) REVERT: U 298 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7635 (mtpt) REVERT: J 305 SER cc_start: 0.8395 (p) cc_final: 0.8137 (p) REVERT: X 310 TYR cc_start: 0.4577 (m-80) cc_final: 0.4055 (t80) REVERT: a 298 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7740 (mmmt) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.8034 time to fit residues: 64.3841 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 : 0.390 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.0170 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.157503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.137897 restraints weight = 3882.756| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.78 r_work: 0.3791 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3825 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= 0.082 Angle : 0.456 5.726 4440 Z= 0.225 Chirality : 0.066 0.152 495 Planarity : 0.005 0.035 555 Dihedral : 7.009 57.356 450 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.94 % Allowed : 18.89 % 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: 0.12 (0.46), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.10 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.020 0.001 TYR O 310 Details of bonding type rmsd hydrogen bonds : bond 0.01361 ( 48) hydrogen bonds : angle 4.46349 ( 144) covalent geometry : bond 0.00203 ( 3300) covalent geometry : angle 0.45625 ( 4440) Misc. bond : bond 0.00015 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.95 seconds wall clock time: 46 minutes 48.83 seconds (2808.83 seconds total)