Starting phenix.real_space_refine on Sat May 2 17:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.map" model { file = "/net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u02_56480/05_2026/9u02_56480.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 C 2410 2.51 5 N 690 2.21 5 O 740 1.98 5 H 3670 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7510 Number of models: 1 Model: "" Number of chains: 1 Chain: "K" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 751 Classifications: {'peptide': 50} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 49} Restraints were copied for chains: L, M, N, O, P, Q, R, S, T Time building chain proxies: 1.05, per 1000 atoms: 0.14 Number of scatterers: 7510 At special positions: 0 Unit cell: (72.52, 101.38, 50.32, 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) O 740 8.00 N 690 7.00 C 2410 6.00 H 3670 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.63 Conformation dependent library (CDL) restraints added in 352.6 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 860 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=15, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=16, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.721A pdb=" N ASN L 9 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN O 9 " --> pdb=" O PHE L 8 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN Q 9 " --> pdb=" O PHE O 8 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN S 9 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'K' and resid 12 through 13 removed outlier: 5.985A pdb=" N VAL K 12 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL L 12 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL O 12 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL Q 12 " --> pdb=" O ALA S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=17 Processing sheet with id=18, first strand: chain 'K' and resid 20 through 25 removed outlier: 6.594A pdb=" N TRP L 21 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL O 24 " --> pdb=" O TRP L 21 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN L 23 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP Q 21 " --> pdb=" O LEU S 22 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL S 24 " --> pdb=" O TRP Q 21 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN Q 23 " --> pdb=" O VAL S 24 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'K' and resid 30 through 37 removed outlier: 6.465A pdb=" N GLU K 31 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY L 34 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR K 33 " --> pdb=" O GLY L 34 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE L 36 " --> pdb=" O THR K 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE K 35 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU L 31 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY O 34 " --> pdb=" O GLU L 31 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR L 33 " --> pdb=" O GLY O 34 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE O 36 " --> pdb=" O THR L 33 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE L 35 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU O 31 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY Q 34 " --> pdb=" O GLU O 31 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR O 33 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE Q 36 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE O 35 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU Q 31 " --> pdb=" O VAL S 32 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY S 34 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR Q 33 " --> pdb=" O GLY S 34 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE S 36 " --> pdb=" O THR Q 33 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE Q 35 " --> pdb=" O ILE S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=19 Processing sheet with id=20, first strand: chain 'K' and resid 41 through 43 Processing sheet with id=21, first strand: chain 'K' and resid 46 through 49 Processing sheet with id=22, first strand: chain 'M' and resid 2 through 3 Processing sheet with id=23, first strand: chain 'M' and resid 7 through 9 removed outlier: 6.721A pdb=" N ASN N 9 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN P 9 " --> pdb=" O PHE N 8 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN R 9 " --> pdb=" O PHE P 8 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN T 9 " --> pdb=" O PHE R 8 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'M' and resid 12 through 13 removed outlier: 5.985A pdb=" N VAL M 12 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL N 12 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL P 12 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL R 12 " --> pdb=" O ALA T 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=24 Processing sheet with id=25, first strand: chain 'M' and resid 20 through 25 removed outlier: 6.597A pdb=" N TRP P 21 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL R 24 " --> pdb=" O TRP P 21 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLN P 23 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 30 through 37 removed outlier: 6.466A pdb=" N GLU M 31 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLY N 34 " --> pdb=" O GLU M 31 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR M 33 " --> pdb=" O GLY N 34 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE N 36 " --> pdb=" O THR M 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE M 35 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU N 31 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY P 34 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR N 33 " --> pdb=" O GLY P 34 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE P 36 " --> pdb=" O THR N 33 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE N 35 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU P 31 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY R 34 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR P 33 " --> pdb=" O GLY R 34 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE R 36 " --> pdb=" O THR P 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE P 35 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU R 31 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLY T 34 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR R 33 " --> pdb=" O GLY T 34 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE T 36 " --> pdb=" O THR R 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE R 35 " --> pdb=" O ILE T 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=26 Processing sheet with id=27, first strand: chain 'M' and resid 41 through 43 Processing sheet with id=28, first strand: chain 'M' and resid 46 through 49 81 hydrogen bonds defined for protein. 243 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: 1.69 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 3670 0.98 - 1.12: 0 1.12 - 1.26: 670 1.26 - 1.40: 1050 1.40 - 1.54: 2190 Bond restraints: 7580 Sorted by residual: bond pdb=" CA GLY L 6 " pdb=" C GLY L 6 " ideal model delta sigma weight residual 1.519 1.514 0.005 8.90e-03 1.26e+04 2.88e-01 bond pdb=" CA GLY S 6 " pdb=" C GLY S 6 " ideal model delta sigma weight residual 1.519 1.514 0.005 8.90e-03 1.26e+04 2.74e-01 bond pdb=" CA GLY P 6 " pdb=" C GLY P 6 " ideal model delta sigma weight residual 1.519 1.514 0.004 8.90e-03 1.26e+04 2.51e-01 bond pdb=" CA GLY T 6 " pdb=" C GLY T 6 " ideal model delta sigma weight residual 1.519 1.514 0.004 8.90e-03 1.26e+04 2.46e-01 bond pdb=" CA GLY N 6 " pdb=" C GLY N 6 " ideal model delta sigma weight residual 1.519 1.514 0.004 8.90e-03 1.26e+04 2.39e-01 ... (remaining 7575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 13490 7.13 - 14.25: 0 14.25 - 21.38: 0 21.38 - 28.50: 0 28.50 - 35.63: 30 Bond angle restraints: 13520 Sorted by residual: angle pdb=" C SER O 29 " pdb=" CA SER O 29 " pdb=" HA SER O 29 " ideal model delta sigma weight residual 109.00 73.37 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER L 29 " pdb=" CA SER L 29 " pdb=" HA SER L 29 " ideal model delta sigma weight residual 109.00 73.40 35.60 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER Q 29 " pdb=" CA SER Q 29 " pdb=" HA SER Q 29 " ideal model delta sigma weight residual 109.00 73.41 35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER N 29 " pdb=" CA SER N 29 " pdb=" HA SER N 29 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER T 29 " pdb=" CA SER T 29 " pdb=" HA SER T 29 " ideal model delta sigma weight residual 109.00 73.43 35.57 3.00e+00 1.11e-01 1.41e+02 ... (remaining 13515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 2993 11.82 - 23.65: 207 23.65 - 35.47: 110 35.47 - 47.30: 90 47.30 - 59.12: 130 Dihedral angle restraints: 3530 sinusoidal: 1860 harmonic: 1670 Sorted by residual: dihedral pdb=" C SER P 29 " pdb=" N SER P 29 " pdb=" CA SER P 29 " pdb=" CB SER P 29 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C SER K 29 " pdb=" N SER K 29 " pdb=" CA SER K 29 " pdb=" CB SER K 29 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C SER M 29 " pdb=" N SER M 29 " pdb=" CA SER M 29 " pdb=" CB SER M 29 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 3527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 469 0.072 - 0.145: 71 0.145 - 0.217: 0 0.217 - 0.290: 0 0.290 - 0.362: 10 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA SER P 29 " pdb=" N SER P 29 " pdb=" C SER P 29 " pdb=" CB SER P 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CA SER K 29 " pdb=" N SER K 29 " pdb=" C SER K 29 " pdb=" CB SER K 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA SER M 29 " pdb=" N SER M 29 " pdb=" C SER M 29 " pdb=" CB SER M 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 547 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 5 " -0.003 2.00e-02 2.50e+03 6.40e-03 4.10e-01 pdb=" C GLN S 5 " 0.011 2.00e-02 2.50e+03 pdb=" O GLN S 5 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY S 6 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN P 5 " 0.003 2.00e-02 2.50e+03 6.34e-03 4.02e-01 pdb=" C GLN P 5 " -0.011 2.00e-02 2.50e+03 pdb=" O GLN P 5 " 0.004 2.00e-02 2.50e+03 pdb=" N GLY P 6 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN O 5 " -0.003 2.00e-02 2.50e+03 6.30e-03 3.97e-01 pdb=" C GLN O 5 " 0.011 2.00e-02 2.50e+03 pdb=" O GLN O 5 " -0.004 2.00e-02 2.50e+03 pdb=" N GLY O 6 " -0.004 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.21: 613 2.21 - 2.78: 14158 2.78 - 3.36: 17941 3.36 - 3.93: 26115 3.93 - 4.50: 37232 Nonbonded interactions: 96059 Sorted by model distance: nonbonded pdb=" H SER T 29 " pdb=" HA SER T 29 " model vdw 1.638 1.816 nonbonded pdb=" H SER S 29 " pdb=" HA SER S 29 " model vdw 1.638 1.816 nonbonded pdb=" H SER P 29 " pdb=" HA SER P 29 " model vdw 1.638 1.816 nonbonded pdb=" H SER L 29 " pdb=" HA SER L 29 " model vdw 1.638 1.816 nonbonded pdb=" H SER O 29 " pdb=" HA SER O 29 " model vdw 1.638 1.816 ... (remaining 96054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 6.000 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0025 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 : 0.003 0.015 3910 Z= 0.150 Angle : 0.468 4.693 5280 Z= 0.277 Chirality : 0.067 0.362 550 Planarity : 0.002 0.011 700 Dihedral : 18.866 59.122 1330 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 0.00 % Allowed : 28.21 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.40), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 1 TYR 0.001 0.000 TYR L 16 PHE 0.003 0.001 PHE R 48 TRP 0.005 0.001 TRP Q 11 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3910) covalent geometry : angle 0.46828 ( 5280) hydrogen bonds : bond 0.20867 ( 81) hydrogen bonds : angle 5.29648 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.5980 time to fit residues: 9.1577 Evaluate side-chains 8 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN ** N 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 ASN P 5 GLN ** P 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 GLN R 23 GLN S 5 GLN T 5 GLN T 23 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.206101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.187900 restraints weight = 14749.212| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 2.57 r_work: 0.4398 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4289 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1072 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3910 Z= 0.289 Angle : 0.865 8.205 5280 Z= 0.475 Chirality : 0.076 0.421 550 Planarity : 0.007 0.073 700 Dihedral : 7.081 20.835 520 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 11.03 % Allowed : 21.54 % Favored : 67.44 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.30), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG Q 41 TYR 0.017 0.003 TYR P 16 PHE 0.031 0.004 PHE M 43 TRP 0.023 0.003 TRP T 21 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 3910) covalent geometry : angle 0.86457 ( 5280) hydrogen bonds : bond 0.05182 ( 81) hydrogen bonds : angle 6.12139 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 10 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 9 ASN cc_start: 0.0135 (OUTLIER) cc_final: -0.0710 (t0) REVERT: L 30 LYS cc_start: 0.1873 (OUTLIER) cc_final: -0.0024 (ptmm) REVERT: N 4 LYS cc_start: 0.0348 (OUTLIER) cc_final: -0.0565 (mtpt) REVERT: N 37 THR cc_start: 0.0859 (OUTLIER) cc_final: 0.0647 (m) REVERT: O 30 LYS cc_start: 0.1096 (OUTLIER) cc_final: -0.0651 (tttt) REVERT: O 47 GLN cc_start: 0.0296 (OUTLIER) cc_final: -0.0467 (mt0) REVERT: Q 30 LYS cc_start: -0.0251 (OUTLIER) cc_final: -0.0844 (ptmt) REVERT: Q 47 GLN cc_start: 0.0821 (OUTLIER) cc_final: 0.0447 (mt0) REVERT: R 4 LYS cc_start: -0.0515 (OUTLIER) cc_final: -0.0982 (mmtt) REVERT: S 30 LYS cc_start: -0.0327 (OUTLIER) cc_final: -0.0590 (ptmt) REVERT: S 47 GLN cc_start: 0.3034 (OUTLIER) cc_final: 0.2642 (mt0) outliers start: 43 outliers final: 17 residues processed: 53 average time/residue: 1.2130 time to fit residues: 66.3602 Evaluate side-chains 35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 7 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 9 ASN Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 47 GLN Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 GLN Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 47 GLN Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 37 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 23 GLN N 23 GLN O 20 GLN P 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.205629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.187734 restraints weight = 14961.389| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 2.57 r_work: 0.4428 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4325 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0989 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3910 Z= 0.100 Angle : 0.498 4.014 5280 Z= 0.291 Chirality : 0.069 0.374 550 Planarity : 0.003 0.035 700 Dihedral : 5.123 15.300 520 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.13 % Allowed : 26.15 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.31), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 1 TYR 0.004 0.001 TYR Q 16 PHE 0.008 0.001 PHE L 8 TRP 0.012 0.002 TRP T 21 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3910) covalent geometry : angle 0.49756 ( 5280) hydrogen bonds : bond 0.03963 ( 81) hydrogen bonds : angle 4.99396 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 10 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.1635 (OUTLIER) cc_final: -0.0110 (ptmm) REVERT: N 4 LYS cc_start: 0.0091 (OUTLIER) cc_final: -0.0803 (mtpm) REVERT: O 30 LYS cc_start: 0.0931 (OUTLIER) cc_final: -0.0622 (OUTLIER) REVERT: P 25 ASP cc_start: 0.1127 (OUTLIER) cc_final: -0.1353 (m-30) REVERT: Q 30 LYS cc_start: -0.0335 (OUTLIER) cc_final: -0.0843 (ptmt) REVERT: S 30 LYS cc_start: -0.0608 (OUTLIER) cc_final: -0.0953 (ptmt) REVERT: S 38 GLN cc_start: 0.3534 (mm-40) cc_final: 0.3327 (mm-40) REVERT: T 5 GLN cc_start: 0.3303 (OUTLIER) cc_final: 0.2424 (tt0) outliers start: 20 outliers final: 8 residues processed: 30 average time/residue: 1.2731 time to fit residues: 39.4993 Evaluate side-chains 22 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 8 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 4 LYS Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 4 LYS Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain T residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 0.0040 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 0.0770 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1354 ------------------------------------------------------------------------------- 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 = 0.4797 r_free = 0.4797 target = 0.218199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.200811 restraints weight = 15235.435| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 2.57 r_work: 0.4543 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4439 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1218 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3910 Z= 0.123 Angle : 0.524 4.109 5280 Z= 0.302 Chirality : 0.069 0.382 550 Planarity : 0.004 0.042 700 Dihedral : 4.733 16.427 520 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 6.67 % Allowed : 25.64 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.31), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 1 TYR 0.008 0.001 TYR P 16 PHE 0.012 0.002 PHE M 48 TRP 0.021 0.002 TRP T 21 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3910) covalent geometry : angle 0.52367 ( 5280) hydrogen bonds : bond 0.02817 ( 81) hydrogen bonds : angle 4.81857 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 9 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 4 LYS cc_start: -0.1239 (OUTLIER) cc_final: -0.2564 (tttt) REVERT: L 30 LYS cc_start: 0.1458 (OUTLIER) cc_final: -0.0245 (tttp) REVERT: M 3 ASP cc_start: 0.0772 (OUTLIER) cc_final: -0.0657 (t70) REVERT: O 30 LYS cc_start: 0.0823 (OUTLIER) cc_final: -0.0685 (tttp) REVERT: P 25 ASP cc_start: 0.1172 (OUTLIER) cc_final: -0.1245 (m-30) REVERT: Q 30 LYS cc_start: -0.0272 (OUTLIER) cc_final: -0.0743 (ptmt) REVERT: S 35 ILE cc_start: -0.0005 (OUTLIER) cc_final: -0.0588 (mt) REVERT: S 46 VAL cc_start: 0.1040 (OUTLIER) cc_final: 0.0524 (t) outliers start: 26 outliers final: 11 residues processed: 35 average time/residue: 1.0442 time to fit residues: 37.9671 Evaluate side-chains 27 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 8 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 5 GLN Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 37 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.242571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.227478 restraints weight = 15379.102| |-----------------------------------------------------------------------------| r_work (start): 0.4834 rms_B_bonded: 2.36 r_work: 0.4773 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4666 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1862 moved from start: 0.9225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 3910 Z= 0.261 Angle : 0.841 6.791 5280 Z= 0.474 Chirality : 0.077 0.403 550 Planarity : 0.009 0.111 700 Dihedral : 7.455 25.576 520 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 9.74 % Allowed : 23.85 % Favored : 66.41 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.43 (0.26), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.20), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG O 41 TYR 0.018 0.003 TYR M 16 PHE 0.032 0.004 PHE Q 8 TRP 0.027 0.004 TRP R 11 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 3910) covalent geometry : angle 0.84114 ( 5280) hydrogen bonds : bond 0.06049 ( 81) hydrogen bonds : angle 6.25753 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 8 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 3 ASP cc_start: 0.4371 (OUTLIER) cc_final: 0.3904 (t0) REVERT: L 30 LYS cc_start: 0.1751 (OUTLIER) cc_final: -0.0156 (tttp) REVERT: L 46 VAL cc_start: 0.0172 (OUTLIER) cc_final: -0.0222 (t) REVERT: N 3 ASP cc_start: 0.1713 (OUTLIER) cc_final: 0.0436 (m-30) REVERT: O 2 LEU cc_start: 0.4303 (OUTLIER) cc_final: 0.3924 (mt) REVERT: O 30 LYS cc_start: 0.1443 (OUTLIER) cc_final: -0.0560 (ptmm) REVERT: O 46 VAL cc_start: -0.0360 (OUTLIER) cc_final: -0.0894 (t) REVERT: P 3 ASP cc_start: 0.2708 (OUTLIER) cc_final: 0.1606 (m-30) REVERT: P 25 ASP cc_start: 0.2047 (OUTLIER) cc_final: -0.1286 (m-30) REVERT: Q 30 LYS cc_start: -0.0185 (OUTLIER) cc_final: -0.0685 (ptmm) REVERT: Q 35 ILE cc_start: -0.0037 (OUTLIER) cc_final: -0.0910 (mp) REVERT: Q 41 ARG cc_start: 0.0648 (ttm-80) cc_final: 0.0056 (ttm110) REVERT: R 3 ASP cc_start: 0.2123 (OUTLIER) cc_final: 0.0878 (m-30) REVERT: T 3 ASP cc_start: 0.2088 (OUTLIER) cc_final: 0.1482 (t0) REVERT: T 12 VAL cc_start: 0.2413 (t) cc_final: 0.0638 (p) outliers start: 38 outliers final: 13 residues processed: 46 average time/residue: 0.8738 time to fit residues: 41.9400 Evaluate side-chains 33 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 7 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 3 ASP Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 4 LYS Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 25 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain T residue 2 LEU Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.249058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.233859 restraints weight = 15408.859| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 2.39 r_work: 0.4826 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4719 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1895 moved from start: 0.9879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3910 Z= 0.182 Angle : 0.647 5.992 5280 Z= 0.370 Chirality : 0.072 0.386 550 Planarity : 0.005 0.062 700 Dihedral : 6.346 21.867 520 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.08 % Favored : 87.71 % Rotamer: Outliers : 7.44 % Allowed : 25.13 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.27), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.20), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 1 TYR 0.009 0.001 TYR T 16 PHE 0.017 0.003 PHE K 43 TRP 0.019 0.003 TRP P 11 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3910) covalent geometry : angle 0.64730 ( 5280) hydrogen bonds : bond 0.04272 ( 81) hydrogen bonds : angle 6.01741 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 6 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 46 VAL cc_start: 0.1179 (OUTLIER) cc_final: 0.0944 (t) REVERT: L 30 LYS cc_start: 0.1692 (OUTLIER) cc_final: -0.0110 (tttm) REVERT: M 3 ASP cc_start: 0.1796 (OUTLIER) cc_final: 0.0505 (t0) REVERT: N 3 ASP cc_start: 0.1737 (OUTLIER) cc_final: 0.0863 (m-30) REVERT: O 30 LYS cc_start: 0.1435 (OUTLIER) cc_final: -0.0427 (tttp) REVERT: P 3 ASP cc_start: 0.2430 (OUTLIER) cc_final: 0.1397 (m-30) REVERT: Q 30 LYS cc_start: -0.0184 (OUTLIER) cc_final: -0.0542 (ptmm) REVERT: Q 35 ILE cc_start: 0.0094 (OUTLIER) cc_final: -0.0932 (mp) REVERT: R 3 ASP cc_start: 0.2253 (OUTLIER) cc_final: 0.1237 (m-30) REVERT: S 35 ILE cc_start: 0.0676 (OUTLIER) cc_final: 0.0219 (mp) REVERT: T 3 ASP cc_start: 0.2288 (OUTLIER) cc_final: 0.1847 (t0) REVERT: T 5 GLN cc_start: 0.4745 (OUTLIER) cc_final: 0.4221 (mp10) REVERT: T 12 VAL cc_start: 0.2401 (t) cc_final: 0.0417 (p) outliers start: 29 outliers final: 11 residues processed: 34 average time/residue: 0.8670 time to fit residues: 30.8704 Evaluate side-chains 29 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 6 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain Q residue 2 LEU Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 37 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 20 GLN L 7 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.254133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.238275 restraints weight = 15426.365| |-----------------------------------------------------------------------------| r_work (start): 0.4936 rms_B_bonded: 2.51 r_work: 0.4877 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.4877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1906 moved from start: 1.0200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3910 Z= 0.131 Angle : 0.565 4.067 5280 Z= 0.326 Chirality : 0.070 0.378 550 Planarity : 0.005 0.060 700 Dihedral : 5.695 18.197 520 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.88 % Favored : 87.92 % Rotamer: Outliers : 5.64 % Allowed : 26.67 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.28), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.21), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 41 TYR 0.008 0.001 TYR N 16 PHE 0.012 0.002 PHE K 43 TRP 0.014 0.002 TRP T 11 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3910) covalent geometry : angle 0.56510 ( 5280) hydrogen bonds : bond 0.03757 ( 81) hydrogen bonds : angle 5.72367 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 6 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.1476 (OUTLIER) cc_final: -0.0184 (tttm) REVERT: N 3 ASP cc_start: 0.1833 (OUTLIER) cc_final: 0.0846 (m-30) REVERT: N 22 LEU cc_start: -0.1623 (OUTLIER) cc_final: -0.1830 (mt) REVERT: O 30 LYS cc_start: 0.1357 (OUTLIER) cc_final: -0.0313 (ttmm) REVERT: P 3 ASP cc_start: 0.2382 (OUTLIER) cc_final: 0.1418 (m-30) REVERT: Q 30 LYS cc_start: -0.0356 (OUTLIER) cc_final: -0.0668 (ptmm) REVERT: R 3 ASP cc_start: 0.2380 (OUTLIER) cc_final: 0.1415 (m-30) REVERT: T 5 GLN cc_start: 0.4279 (OUTLIER) cc_final: 0.3765 (mp10) REVERT: T 12 VAL cc_start: 0.2373 (t) cc_final: 0.0365 (p) outliers start: 22 outliers final: 11 residues processed: 28 average time/residue: 0.9120 time to fit residues: 26.7258 Evaluate side-chains 25 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 6 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain N residue 3 ASP Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.256546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.240826 restraints weight = 15578.317| |-----------------------------------------------------------------------------| r_work (start): 0.4956 rms_B_bonded: 2.51 r_work: 0.4895 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.4895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1929 moved from start: 1.0471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3910 Z= 0.125 Angle : 0.551 4.293 5280 Z= 0.318 Chirality : 0.070 0.373 550 Planarity : 0.004 0.039 700 Dihedral : 5.399 17.571 520 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 5.38 % Allowed : 26.41 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.11 (0.28), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 41 TYR 0.006 0.001 TYR N 16 PHE 0.011 0.002 PHE L 43 TRP 0.011 0.002 TRP R 11 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 3910) covalent geometry : angle 0.55131 ( 5280) hydrogen bonds : bond 0.03438 ( 81) hydrogen bonds : angle 5.58372 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 7 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.1549 (OUTLIER) cc_final: -0.0148 (tttm) REVERT: N 22 LEU cc_start: -0.1572 (OUTLIER) cc_final: -0.1777 (mt) REVERT: O 30 LYS cc_start: 0.1275 (OUTLIER) cc_final: -0.0390 (tttp) REVERT: P 3 ASP cc_start: 0.2577 (OUTLIER) cc_final: 0.1570 (m-30) REVERT: Q 30 LYS cc_start: -0.0330 (OUTLIER) cc_final: -0.0710 (ptmm) REVERT: R 3 ASP cc_start: 0.2376 (OUTLIER) cc_final: 0.1426 (m-30) REVERT: R 4 LYS cc_start: 0.0654 (tttm) cc_final: -0.0079 (tptm) REVERT: T 12 VAL cc_start: 0.2453 (t) cc_final: 0.0530 (p) outliers start: 21 outliers final: 13 residues processed: 28 average time/residue: 1.0032 time to fit residues: 29.3364 Evaluate side-chains 25 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 6 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 3 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5114 r_free = 0.5114 target = 0.256916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.241664 restraints weight = 15353.579| |-----------------------------------------------------------------------------| r_work (start): 0.4966 rms_B_bonded: 2.44 r_work: 0.4907 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4803 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1823 moved from start: 1.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3910 Z= 0.100 Angle : 0.512 3.896 5280 Z= 0.297 Chirality : 0.069 0.372 550 Planarity : 0.003 0.037 700 Dihedral : 5.047 15.212 520 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.62 % Allowed : 26.67 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.29), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.22), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 41 TYR 0.006 0.001 TYR R 16 PHE 0.009 0.001 PHE L 43 TRP 0.010 0.001 TRP T 11 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3910) covalent geometry : angle 0.51166 ( 5280) hydrogen bonds : bond 0.03126 ( 81) hydrogen bonds : angle 5.36018 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 5 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.1463 (OUTLIER) cc_final: -0.0129 (tttm) REVERT: O 30 LYS cc_start: 0.1237 (OUTLIER) cc_final: -0.0431 (tttp) REVERT: P 3 ASP cc_start: 0.2567 (OUTLIER) cc_final: 0.1474 (m-30) REVERT: Q 30 LYS cc_start: -0.0532 (OUTLIER) cc_final: -0.0789 (ptmm) REVERT: R 3 ASP cc_start: 0.2327 (OUTLIER) cc_final: 0.1299 (m-30) REVERT: R 4 LYS cc_start: 0.0301 (tttm) cc_final: -0.0386 (tptm) REVERT: T 5 GLN cc_start: 0.4087 (OUTLIER) cc_final: 0.3685 (mp10) outliers start: 18 outliers final: 11 residues processed: 22 average time/residue: 1.1676 time to fit residues: 26.6795 Evaluate side-chains 22 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 5 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 3 ASP Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 30 LYS Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 4 LYS Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.258845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.243525 restraints weight = 15336.262| |-----------------------------------------------------------------------------| r_work (start): 0.4983 rms_B_bonded: 2.44 r_work: 0.4919 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.4813 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1820 moved from start: 1.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3910 Z= 0.095 Angle : 0.501 3.972 5280 Z= 0.290 Chirality : 0.069 0.367 550 Planarity : 0.003 0.029 700 Dihedral : 4.728 14.588 520 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 3.33 % Allowed : 27.95 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.30), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 41 TYR 0.006 0.001 TYR R 16 PHE 0.009 0.001 PHE L 43 TRP 0.008 0.001 TRP P 21 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3910) covalent geometry : angle 0.50144 ( 5280) hydrogen bonds : bond 0.02860 ( 81) hydrogen bonds : angle 5.16492 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.1419 (OUTLIER) cc_final: -0.0162 (tttm) REVERT: O 30 LYS cc_start: 0.1170 (OUTLIER) cc_final: -0.0426 (tttm) REVERT: R 3 ASP cc_start: 0.2334 (OUTLIER) cc_final: 0.1390 (m-30) REVERT: R 4 LYS cc_start: 0.0469 (tttm) cc_final: -0.0199 (tptm) REVERT: T 5 GLN cc_start: 0.4001 (OUTLIER) cc_final: 0.3473 (mp10) outliers start: 13 outliers final: 9 residues processed: 18 average time/residue: 1.1272 time to fit residues: 21.2030 Evaluate side-chains 18 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 5 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain N residue 30 LYS Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 30 LYS Chi-restraints excluded: chain O residue 38 GLN Chi-restraints excluded: chain P residue 30 LYS Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain T residue 3 ASP Chi-restraints excluded: chain T residue 5 GLN Chi-restraints excluded: chain T residue 33 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.260141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.244458 restraints weight = 15378.975| |-----------------------------------------------------------------------------| r_work (start): 0.4995 rms_B_bonded: 2.46 r_work: 0.4934 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4828 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1828 moved from start: 1.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3910 Z= 0.093 Angle : 0.494 3.789 5280 Z= 0.287 Chirality : 0.069 0.368 550 Planarity : 0.003 0.031 700 Dihedral : 4.676 14.079 520 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.33 % Allowed : 27.95 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.31), residues: 480 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 41 TYR 0.006 0.001 TYR R 16 PHE 0.009 0.001 PHE L 43 TRP 0.009 0.001 TRP T 11 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3910) covalent geometry : angle 0.49440 ( 5280) hydrogen bonds : bond 0.02818 ( 81) hydrogen bonds : angle 5.03754 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2977.64 seconds wall clock time: 51 minutes 12.49 seconds (3072.49 seconds total)