Starting phenix.real_space_refine on Mon Jul 6 04:40:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0l_66437/07_2026/9x0l_66437.map" } resolution = 2.17 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= 0.021 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 216 5.16 5 C 21168 2.51 5 N 5568 2.21 5 O 6384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 288 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33336 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1389 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y Time building chain proxies: 2.59, per 1000 atoms: 0.08 Number of scatterers: 33336 At special positions: 0 Unit cell: (126.5, 126.5, 126.5, 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 216 16.00 O 6384 8.00 N 5568 7.00 C 21168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7728 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 93 through 122 Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 135 through 157 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'B' and resid 11 through 39 Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 93 through 122 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 135 through 157 Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'C' and resid 11 through 39 Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 93 through 122 Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 135 through 157 Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'D' and resid 11 through 39 Processing helix chain 'D' and resid 46 through 74 Processing helix chain 'D' and resid 93 through 122 Processing helix chain 'D' and resid 124 through 135 Processing helix chain 'D' and resid 135 through 157 Processing helix chain 'D' and resid 159 through 169 Processing helix chain 'E' and resid 11 through 39 Processing helix chain 'E' and resid 46 through 74 Processing helix chain 'E' and resid 93 through 122 Processing helix chain 'E' and resid 124 through 135 Processing helix chain 'E' and resid 135 through 157 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'F' and resid 11 through 39 Processing helix chain 'F' and resid 46 through 74 Processing helix chain 'F' and resid 93 through 122 Processing helix chain 'F' and resid 124 through 135 Processing helix chain 'F' and resid 135 through 157 Processing helix chain 'F' and resid 159 through 169 Processing helix chain 'G' and resid 11 through 39 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 93 through 122 Processing helix chain 'G' and resid 124 through 135 Processing helix chain 'G' and resid 135 through 157 Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'H' and resid 11 through 39 Processing helix chain 'H' and resid 46 through 74 Processing helix chain 'H' and resid 93 through 122 Processing helix chain 'H' and resid 124 through 135 Processing helix chain 'H' and resid 135 through 157 Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'I' and resid 11 through 39 Processing helix chain 'I' and resid 46 through 74 Processing helix chain 'I' and resid 93 through 122 Processing helix chain 'I' and resid 124 through 135 Processing helix chain 'I' and resid 135 through 157 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'J' and resid 11 through 39 Processing helix chain 'J' and resid 46 through 74 Processing helix chain 'J' and resid 93 through 122 Processing helix chain 'J' and resid 124 through 135 Processing helix chain 'J' and resid 135 through 157 Processing helix chain 'J' and resid 159 through 169 Processing helix chain 'K' and resid 11 through 39 Processing helix chain 'K' and resid 46 through 74 Processing helix chain 'K' and resid 93 through 122 Processing helix chain 'K' and resid 124 through 135 Processing helix chain 'K' and resid 135 through 157 Processing helix chain 'K' and resid 159 through 169 Processing helix chain 'L' and resid 11 through 39 Processing helix chain 'L' and resid 46 through 74 Processing helix chain 'L' and resid 93 through 122 Processing helix chain 'L' and resid 124 through 135 Processing helix chain 'L' and resid 135 through 157 Processing helix chain 'L' and resid 159 through 169 Processing helix chain 'M' and resid 11 through 39 Processing helix chain 'M' and resid 46 through 74 Processing helix chain 'M' and resid 93 through 122 Processing helix chain 'M' and resid 124 through 135 Processing helix chain 'M' and resid 135 through 157 Processing helix chain 'M' and resid 159 through 169 Processing helix chain 'N' and resid 11 through 39 Processing helix chain 'N' and resid 46 through 74 Processing helix chain 'N' and resid 93 through 122 Processing helix chain 'N' and resid 124 through 135 Processing helix chain 'N' and resid 135 through 157 Processing helix chain 'N' and resid 159 through 169 Processing helix chain 'O' and resid 11 through 39 Processing helix chain 'O' and resid 46 through 74 Processing helix chain 'O' and resid 93 through 122 Processing helix chain 'O' and resid 124 through 135 Processing helix chain 'O' and resid 135 through 157 Processing helix chain 'O' and resid 159 through 169 Processing helix chain 'P' and resid 11 through 39 Processing helix chain 'P' and resid 46 through 74 Processing helix chain 'P' and resid 93 through 122 Processing helix chain 'P' and resid 124 through 135 Processing helix chain 'P' and resid 135 through 157 Processing helix chain 'P' and resid 159 through 169 Processing helix chain 'Q' and resid 11 through 39 Processing helix chain 'Q' and resid 46 through 74 Processing helix chain 'Q' and resid 93 through 122 Processing helix chain 'Q' and resid 124 through 135 Processing helix chain 'Q' and resid 135 through 157 Processing helix chain 'Q' and resid 159 through 169 Processing helix chain 'R' and resid 11 through 39 Processing helix chain 'R' and resid 46 through 74 Processing helix chain 'R' and resid 93 through 122 Processing helix chain 'R' and resid 124 through 135 Processing helix chain 'R' and resid 135 through 157 Processing helix chain 'R' and resid 159 through 169 Processing helix chain 'S' and resid 11 through 39 Processing helix chain 'S' and resid 46 through 74 Processing helix chain 'S' and resid 93 through 122 Processing helix chain 'S' and resid 124 through 135 Processing helix chain 'S' and resid 135 through 157 Processing helix chain 'S' and resid 159 through 169 Processing helix chain 'T' and resid 11 through 39 Processing helix chain 'T' and resid 46 through 74 Processing helix chain 'T' and resid 93 through 122 Processing helix chain 'T' and resid 124 through 135 Processing helix chain 'T' and resid 135 through 157 Processing helix chain 'T' and resid 159 through 169 Processing helix chain 'V' and resid 11 through 39 Processing helix chain 'V' and resid 46 through 74 Processing helix chain 'V' and resid 93 through 122 Processing helix chain 'V' and resid 124 through 135 Processing helix chain 'V' and resid 135 through 157 Processing helix chain 'V' and resid 159 through 169 Processing helix chain 'W' and resid 11 through 39 Processing helix chain 'W' and resid 46 through 74 Processing helix chain 'W' and resid 93 through 122 Processing helix chain 'W' and resid 124 through 135 Processing helix chain 'W' and resid 135 through 157 Processing helix chain 'W' and resid 159 through 169 Processing helix chain 'X' and resid 11 through 39 Processing helix chain 'X' and resid 46 through 74 Processing helix chain 'X' and resid 93 through 122 Processing helix chain 'X' and resid 124 through 135 Processing helix chain 'X' and resid 135 through 157 Processing helix chain 'X' and resid 159 through 169 Processing helix chain 'Y' and resid 11 through 39 Processing helix chain 'Y' and resid 46 through 74 Processing helix chain 'Y' and resid 93 through 122 Processing helix chain 'Y' and resid 124 through 135 Processing helix chain 'Y' and resid 135 through 157 Processing helix chain 'Y' and resid 159 through 169 2640 hydrogen bonds defined for protein. 7920 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: 5.63 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6168 1.32 - 1.44: 8664 1.44 - 1.56: 18816 1.56 - 1.69: 0 1.69 - 1.81: 360 Bond restraints: 34008 Sorted by residual: bond pdb=" CA SER E 34 " pdb=" CB SER E 34 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.28e+01 bond pdb=" CA SER S 34 " pdb=" CB SER S 34 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.28e+01 bond pdb=" CA SER W 34 " pdb=" CB SER W 34 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.28e+01 bond pdb=" CA SER A 34 " pdb=" CB SER A 34 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.28e+01 bond pdb=" CA SER L 34 " pdb=" CB SER L 34 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.55e-02 4.16e+03 1.28e+01 ... (remaining 34003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 27576 1.41 - 2.83: 12912 2.83 - 4.24: 4488 4.24 - 5.65: 672 5.65 - 7.07: 96 Bond angle restraints: 45744 Sorted by residual: angle pdb=" N LEU E 170 " pdb=" CA LEU E 170 " pdb=" C LEU E 170 " ideal model delta sigma weight residual 113.02 107.17 5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" N LEU S 170 " pdb=" CA LEU S 170 " pdb=" C LEU S 170 " ideal model delta sigma weight residual 113.02 107.17 5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" N LEU W 170 " pdb=" CA LEU W 170 " pdb=" C LEU W 170 " ideal model delta sigma weight residual 113.02 107.17 5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" N LEU D 170 " pdb=" CA LEU D 170 " pdb=" C LEU D 170 " ideal model delta sigma weight residual 113.02 107.17 5.85 1.20e+00 6.94e-01 2.38e+01 angle pdb=" N LEU G 170 " pdb=" CA LEU G 170 " pdb=" C LEU G 170 " ideal model delta sigma weight residual 113.02 107.17 5.85 1.20e+00 6.94e-01 2.38e+01 ... (remaining 45739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 18504 17.49 - 34.97: 1560 34.97 - 52.45: 336 52.45 - 69.94: 72 69.94 - 87.42: 24 Dihedral angle restraints: 20496 sinusoidal: 8544 harmonic: 11952 Sorted by residual: dihedral pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " pdb=" CD GLU B 111 " pdb=" OE1 GLU B 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.42 -87.42 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU Q 111 " pdb=" CG GLU Q 111 " pdb=" CD GLU Q 111 " pdb=" OE1 GLU Q 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.42 -87.42 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU X 111 " pdb=" CG GLU X 111 " pdb=" CD GLU X 111 " pdb=" OE1 GLU X 111 " ideal model delta sinusoidal sigma weight residual 0.00 87.42 -87.42 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 20493 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.041: 1944 0.041 - 0.081: 1224 0.081 - 0.120: 1080 0.120 - 0.160: 408 0.160 - 0.200: 144 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CB VAL H 156 " pdb=" CA VAL H 156 " pdb=" CG1 VAL H 156 " pdb=" CG2 VAL H 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL J 156 " pdb=" CA VAL J 156 " pdb=" CG1 VAL J 156 " pdb=" CG2 VAL J 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL K 156 " pdb=" CA VAL K 156 " pdb=" CG1 VAL K 156 " pdb=" CG2 VAL K 156 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 4797 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS O 167 " -0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C HIS O 167 " 0.044 2.00e-02 2.50e+03 pdb=" O HIS O 167 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU O 168 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS K 167 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C HIS K 167 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS K 167 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU K 168 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS M 167 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C HIS M 167 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS M 167 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU M 168 " 0.015 2.00e-02 2.50e+03 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6072 2.79 - 3.32: 37224 3.32 - 3.85: 62292 3.85 - 4.37: 79020 4.37 - 4.90: 123096 Nonbonded interactions: 307704 Sorted by model distance: nonbonded pdb=" OH TYR B 30 " pdb=" O GLN D 81 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 30 " pdb=" O GLN F 81 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR C 30 " pdb=" O GLN J 81 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR Q 30 " pdb=" O GLN R 81 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR H 30 " pdb=" O GLN I 81 " model vdw 2.265 3.040 ... (remaining 307699 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = 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' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 1.080 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.060 Process input model: 21.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 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 : 0.012 0.055 34008 Z= 0.855 Angle : 1.739 7.069 45744 Z= 1.364 Chirality : 0.077 0.200 4800 Planarity : 0.005 0.025 5904 Dihedral : 14.074 87.421 12768 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.13), residues: 4032 helix: 0.89 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.45 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 41 TYR 0.016 0.004 TYR J 149 PHE 0.018 0.004 PHE I 52 TRP 0.023 0.003 TRP C 37 HIS 0.003 0.002 HIS F 116 Details of bonding type rmsd/Z covalent geometry : bond 0.01182 / 0.86 (34008) covalent geometry : angle 1.73887 / 1.36 (45744) hydrogen bonds : bond 0.17282 / 11.31 ( 2640) hydrogen bonds : angle 6.28651 / 4.65 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 984 time to evaluate : 1.145 Fit side-chains REVERT: A 82 ASP cc_start: 0.7878 (m-30) cc_final: 0.7562 (m-30) REVERT: A 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: A 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: A 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (tp30) REVERT: B 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7563 (m-30) REVERT: B 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: B 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8551 (ttp) REVERT: B 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8010 (tp30) REVERT: C 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: C 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: C 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: C 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) REVERT: D 82 ASP cc_start: 0.7874 (m-30) cc_final: 0.7560 (m-30) REVERT: D 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8636 (mmtm) REVERT: D 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8550 (ttp) REVERT: D 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) REVERT: E 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7560 (m-30) REVERT: E 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: E 104 MET cc_start: 0.8939 (ttm) cc_final: 0.8550 (ttp) REVERT: E 138 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8011 (tp30) REVERT: F 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: F 84 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8635 (mmtm) REVERT: F 104 MET cc_start: 0.8944 (ttm) cc_final: 0.8555 (ttp) REVERT: F 138 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8007 (tp30) REVERT: G 82 ASP cc_start: 0.7875 (m-30) cc_final: 0.7558 (m-30) REVERT: G 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: G 104 MET cc_start: 0.8943 (ttm) cc_final: 0.8554 (ttp) REVERT: G 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8008 (tp30) REVERT: H 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7561 (m-30) REVERT: H 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8635 (mmtm) REVERT: H 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8549 (ttp) REVERT: H 138 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8006 (tp30) REVERT: I 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: I 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: I 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: I 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) REVERT: J 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7561 (m-30) REVERT: J 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8635 (mmtm) REVERT: J 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8549 (ttp) REVERT: J 138 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8006 (tp30) REVERT: K 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7561 (m-30) REVERT: K 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8635 (mmtm) REVERT: K 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8549 (ttp) REVERT: K 138 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8006 (tp30) REVERT: L 82 ASP cc_start: 0.7878 (m-30) cc_final: 0.7562 (m-30) REVERT: L 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: L 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: L 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (tp30) REVERT: M 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: M 84 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8635 (mmtm) REVERT: M 104 MET cc_start: 0.8944 (ttm) cc_final: 0.8555 (ttp) REVERT: M 138 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8007 (tp30) REVERT: N 82 ASP cc_start: 0.7875 (m-30) cc_final: 0.7558 (m-30) REVERT: N 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: N 104 MET cc_start: 0.8943 (ttm) cc_final: 0.8554 (ttp) REVERT: N 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8008 (tp30) REVERT: O 82 ASP cc_start: 0.7878 (m-30) cc_final: 0.7562 (m-30) REVERT: O 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: O 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: O 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (tp30) REVERT: P 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: P 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: P 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8551 (ttp) REVERT: P 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) REVERT: Q 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7563 (m-30) REVERT: Q 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: Q 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8551 (ttp) REVERT: Q 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8010 (tp30) REVERT: R 82 ASP cc_start: 0.7874 (m-30) cc_final: 0.7560 (m-30) REVERT: R 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8636 (mmtm) REVERT: R 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8550 (ttp) REVERT: R 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) REVERT: S 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7560 (m-30) REVERT: S 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: S 104 MET cc_start: 0.8939 (ttm) cc_final: 0.8550 (ttp) REVERT: S 138 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8011 (tp30) REVERT: T 82 ASP cc_start: 0.7875 (m-30) cc_final: 0.7558 (m-30) REVERT: T 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: T 104 MET cc_start: 0.8943 (ttm) cc_final: 0.8554 (ttp) REVERT: T 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8008 (tp30) REVERT: V 82 ASP cc_start: 0.7877 (m-30) cc_final: 0.7560 (m-30) REVERT: V 84 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8635 (mmtm) REVERT: V 104 MET cc_start: 0.8944 (ttm) cc_final: 0.8555 (ttp) REVERT: V 138 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8007 (tp30) REVERT: W 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7560 (m-30) REVERT: W 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8636 (mmtm) REVERT: W 104 MET cc_start: 0.8939 (ttm) cc_final: 0.8550 (ttp) REVERT: W 138 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8011 (tp30) REVERT: X 82 ASP cc_start: 0.7876 (m-30) cc_final: 0.7563 (m-30) REVERT: X 84 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8635 (mmtm) REVERT: X 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8551 (ttp) REVERT: X 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8010 (tp30) REVERT: Y 82 ASP cc_start: 0.7874 (m-30) cc_final: 0.7560 (m-30) REVERT: Y 84 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8636 (mmtm) REVERT: Y 104 MET cc_start: 0.8941 (ttm) cc_final: 0.8550 (ttp) REVERT: Y 138 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8007 (tp30) outliers start: 0 outliers final: 0 residues processed: 984 average time/residue: 0.8006 time to fit residues: 906.4697 Evaluate side-chains 576 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 81 GLN B 9 ASN B 81 GLN C 9 ASN C 81 GLN D 9 ASN D 81 GLN E 9 ASN E 81 GLN F 9 ASN F 81 GLN G 9 ASN G 81 GLN H 9 ASN H 81 GLN I 9 ASN I 81 GLN J 9 ASN J 81 GLN K 9 ASN K 81 GLN L 9 ASN L 81 GLN M 9 ASN M 81 GLN N 9 ASN N 81 GLN O 9 ASN O 81 GLN P 9 ASN P 81 GLN Q 9 ASN Q 81 GLN R 9 ASN R 81 GLN S 9 ASN S 81 GLN T 9 ASN T 81 GLN V 9 ASN V 81 GLN W 9 ASN W 81 GLN X 9 ASN X 81 GLN Y 9 ASN Y 81 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.085575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.076852 restraints weight = 36934.121| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.33 r_work: 0.2664 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9335 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34008 Z= 0.174 Angle : 0.478 5.078 45744 Z= 0.265 Chirality : 0.037 0.120 4800 Planarity : 0.003 0.016 5904 Dihedral : 3.926 14.590 4392 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.13), residues: 4032 helix: 2.81 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.80 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 85 TYR 0.012 0.002 TYR B 163 PHE 0.016 0.003 PHE I 39 TRP 0.016 0.002 TRP K 37 HIS 0.003 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (34008) covalent geometry : angle 0.47825 / 0.27 (45744) hydrogen bonds : bond 0.04087 / 2.66 ( 2640) hydrogen bonds : angle 3.35390 / 2.47 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 552 time to evaluate : 1.199 Fit side-chains REVERT: A 85 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: A 104 MET cc_start: 0.9019 (ttm) cc_final: 0.8817 (ttp) REVERT: A 138 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8204 (tp30) REVERT: B 85 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8455 (ptm-80) REVERT: B 138 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8207 (tp30) REVERT: C 85 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8447 (ptm-80) REVERT: C 138 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8200 (tp30) REVERT: D 85 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8438 (ptm-80) REVERT: D 138 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8198 (tp30) REVERT: E 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: E 138 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8205 (tp30) REVERT: F 85 ARG cc_start: 0.8694 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: F 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8200 (tp30) REVERT: G 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: G 138 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8209 (tp30) REVERT: H 85 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: H 104 MET cc_start: 0.9021 (ttm) cc_final: 0.8818 (ttp) REVERT: H 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8198 (tp30) REVERT: I 85 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8447 (ptm-80) REVERT: I 138 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8200 (tp30) REVERT: J 85 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: J 104 MET cc_start: 0.9021 (ttm) cc_final: 0.8818 (ttp) REVERT: J 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8198 (tp30) REVERT: K 85 ARG cc_start: 0.8691 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: K 104 MET cc_start: 0.9021 (ttm) cc_final: 0.8818 (ttp) REVERT: K 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8198 (tp30) REVERT: L 85 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: L 104 MET cc_start: 0.9019 (ttm) cc_final: 0.8817 (ttp) REVERT: L 138 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8204 (tp30) REVERT: M 85 ARG cc_start: 0.8694 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: M 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8200 (tp30) REVERT: N 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8450 (ptm-80) REVERT: N 138 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8209 (tp30) REVERT: O 85 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8452 (ptm-80) REVERT: O 104 MET cc_start: 0.9018 (ttm) cc_final: 0.8817 (ttp) REVERT: O 138 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8204 (tp30) REVERT: P 85 ARG cc_start: 0.8700 (ptm-80) cc_final: 0.8447 (ptm-80) REVERT: P 138 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8200 (tp30) REVERT: Q 85 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8455 (ptm-80) REVERT: Q 138 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8207 (tp30) REVERT: R 85 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8438 (ptm-80) REVERT: R 138 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8199 (tp30) REVERT: S 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: S 138 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8205 (tp30) REVERT: T 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: T 138 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8209 (tp30) REVERT: V 85 ARG cc_start: 0.8694 (ptm-80) cc_final: 0.8440 (ptm-80) REVERT: V 138 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8200 (tp30) REVERT: W 85 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8448 (ptm-80) REVERT: W 138 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8205 (tp30) REVERT: X 85 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8455 (ptm-80) REVERT: X 138 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8207 (tp30) REVERT: Y 85 ARG cc_start: 0.8692 (ptm-80) cc_final: 0.8438 (ptm-80) REVERT: Y 138 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8198 (tp30) outliers start: 72 outliers final: 0 residues processed: 552 average time/residue: 0.7833 time to fit residues: 499.2122 Evaluate side-chains 552 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 227 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 40.0000 chunk 356 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 180 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.082658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.073518 restraints weight = 38311.692| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.38 r_work: 0.2616 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9349 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 34008 Z= 0.198 Angle : 0.463 4.705 45744 Z= 0.257 Chirality : 0.038 0.106 4800 Planarity : 0.003 0.017 5904 Dihedral : 3.952 15.096 4392 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.00 % Allowed : 13.33 % Favored : 84.67 % 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: 4.35 (0.13), residues: 4032 helix: 3.29 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 1.01 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 85 TYR 0.011 0.002 TYR L 163 PHE 0.015 0.003 PHE Q 39 TRP 0.015 0.002 TRP K 37 HIS 0.003 0.001 HIS N 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (34008) covalent geometry : angle 0.46256 / 0.26 (45744) hydrogen bonds : bond 0.04111 / 2.68 ( 2640) hydrogen bonds : angle 3.27934 / 2.41 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 504 time to evaluate : 1.058 Fit side-chains REVERT: A 138 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8234 (tp30) REVERT: B 138 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8235 (tp30) REVERT: E 138 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8236 (tp30) REVERT: G 138 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8231 (tp30) REVERT: L 138 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8234 (tp30) REVERT: N 138 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8231 (tp30) REVERT: O 138 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8234 (tp30) REVERT: Q 138 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8235 (tp30) REVERT: S 138 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8236 (tp30) REVERT: T 138 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8231 (tp30) REVERT: W 138 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8236 (tp30) REVERT: X 138 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8235 (tp30) outliers start: 72 outliers final: 0 residues processed: 552 average time/residue: 0.7684 time to fit residues: 491.1897 Evaluate side-chains 504 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 230 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 391 optimal weight: 0.3980 chunk 269 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 189 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 297 optimal weight: 0.0050 overall best weight: 3.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.085475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.076772 restraints weight = 37307.574| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.35 r_work: 0.2668 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9329 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34008 Z= 0.132 Angle : 0.417 4.234 45744 Z= 0.232 Chirality : 0.036 0.104 4800 Planarity : 0.003 0.027 5904 Dihedral : 3.846 14.064 4392 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 16.17 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.69 (0.13), residues: 4032 helix: 3.55 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 1.02 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 85 TYR 0.011 0.001 TYR I 163 PHE 0.012 0.002 PHE H 135 TRP 0.015 0.001 TRP T 37 HIS 0.002 0.001 HIS G 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (34008) covalent geometry : angle 0.41665 / 0.23 (45744) hydrogen bonds : bond 0.03543 / 2.31 ( 2640) hydrogen bonds : angle 3.17317 / 2.34 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 540 time to evaluate : 1.073 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 540 average time/residue: 0.7398 time to fit residues: 466.3240 Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 262 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 130 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 166 optimal weight: 0.4980 overall best weight: 6.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.083124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.074042 restraints weight = 38109.906| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.39 r_work: 0.2635 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9344 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34008 Z= 0.182 Angle : 0.449 4.306 45744 Z= 0.251 Chirality : 0.038 0.107 4800 Planarity : 0.003 0.029 5904 Dihedral : 3.889 14.687 4392 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.33 % Allowed : 14.83 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.51 (0.13), residues: 4032 helix: 3.43 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.93 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 85 TYR 0.010 0.001 TYR J 163 PHE 0.013 0.002 PHE I 39 TRP 0.014 0.002 TRP A 37 HIS 0.003 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (34008) covalent geometry : angle 0.44891 / 0.25 (45744) hydrogen bonds : bond 0.03863 / 2.52 ( 2640) hydrogen bonds : angle 3.25366 / 2.40 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 480 time to evaluate : 1.289 Fit side-chains outliers start: 48 outliers final: 0 residues processed: 504 average time/residue: 0.7929 time to fit residues: 460.9561 Evaluate side-chains 456 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 318 optimal weight: 1.9990 chunk 313 optimal weight: 6.9990 chunk 358 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 280 optimal weight: 40.0000 chunk 314 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.083617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.074535 restraints weight = 38049.288| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.39 r_work: 0.2644 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9341 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34008 Z= 0.164 Angle : 0.434 3.956 45744 Z= 0.242 Chirality : 0.037 0.104 4800 Planarity : 0.003 0.029 5904 Dihedral : 3.858 14.468 4392 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 14.67 % Favored : 84.67 % 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: 4.59 (0.13), residues: 4032 helix: 3.49 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.92 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 85 TYR 0.010 0.001 TYR D 163 PHE 0.013 0.002 PHE T 39 TRP 0.014 0.002 TRP P 37 HIS 0.003 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (34008) covalent geometry : angle 0.43433 / 0.24 (45744) hydrogen bonds : bond 0.03722 / 2.42 ( 2640) hydrogen bonds : angle 3.22875 / 2.38 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 1.467 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 480 average time/residue: 0.9447 time to fit residues: 519.6830 Evaluate side-chains 468 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 194 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 234 optimal weight: 10.0000 chunk 407 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 406 optimal weight: 5.9990 chunk 25 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.084477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.075345 restraints weight = 38291.318| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.40 r_work: 0.2661 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9332 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34008 Z= 0.136 Angle : 0.413 3.860 45744 Z= 0.231 Chirality : 0.036 0.102 4800 Planarity : 0.003 0.031 5904 Dihedral : 3.795 13.830 4392 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.67 % Allowed : 14.67 % Favored : 84.67 % 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: 4.70 (0.13), residues: 4032 helix: 3.58 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.87 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 85 TYR 0.010 0.001 TYR N 163 PHE 0.011 0.002 PHE J 39 TRP 0.014 0.001 TRP P 37 HIS 0.002 0.001 HIS E 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (34008) covalent geometry : angle 0.41340 / 0.23 (45744) hydrogen bonds : bond 0.03491 / 2.27 ( 2640) hydrogen bonds : angle 3.18593 / 2.35 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 504 time to evaluate : 1.353 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 504 average time/residue: 0.8046 time to fit residues: 471.6829 Evaluate side-chains 492 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 70 optimal weight: 20.0000 chunk 320 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 310 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.082879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.073827 restraints weight = 38277.901| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.39 r_work: 0.2630 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9346 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 34008 Z= 0.200 Angle : 0.456 4.168 45744 Z= 0.255 Chirality : 0.039 0.108 4800 Planarity : 0.003 0.031 5904 Dihedral : 3.891 14.896 4392 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.67 % Allowed : 14.67 % Favored : 84.67 % 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: 4.49 (0.13), residues: 4032 helix: 3.42 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.92 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 85 TYR 0.011 0.001 TYR H 163 PHE 0.014 0.002 PHE T 39 TRP 0.013 0.002 TRP K 37 HIS 0.003 0.001 HIS P 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (34008) covalent geometry : angle 0.45567 / 0.25 (45744) hydrogen bonds : bond 0.03922 / 2.55 ( 2640) hydrogen bonds : angle 3.26873 / 2.41 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 444 time to evaluate : 1.407 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 444 average time/residue: 0.8493 time to fit residues: 435.3409 Evaluate side-chains 432 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 346 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 chunk 254 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 271 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.082507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.073543 restraints weight = 38356.845| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.37 r_work: 0.2633 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9348 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 34008 Z= 0.196 Angle : 0.453 4.008 45744 Z= 0.253 Chirality : 0.038 0.108 4800 Planarity : 0.003 0.031 5904 Dihedral : 3.894 14.945 4392 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.48 (0.13), residues: 4032 helix: 3.41 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.92 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 85 TYR 0.011 0.001 TYR W 163 PHE 0.013 0.002 PHE R 39 TRP 0.014 0.002 TRP S 37 HIS 0.003 0.001 HIS H 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (34008) covalent geometry : angle 0.45330 / 0.25 (45744) hydrogen bonds : bond 0.03907 / 2.54 ( 2640) hydrogen bonds : angle 3.26608 / 2.41 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.8805 time to fit residues: 439.6355 Evaluate side-chains 432 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 45 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 369 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.083421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.074340 restraints weight = 38363.522| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.40 r_work: 0.2640 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9342 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34008 Z= 0.168 Angle : 0.440 4.105 45744 Z= 0.246 Chirality : 0.037 0.105 4800 Planarity : 0.003 0.032 5904 Dihedral : 3.864 14.637 4392 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.53 (0.13), residues: 4032 helix: 3.45 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.89 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 85 TYR 0.011 0.001 TYR O 163 PHE 0.013 0.002 PHE O 39 TRP 0.015 0.002 TRP J 37 HIS 0.003 0.001 HIS J 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (34008) covalent geometry : angle 0.43975 / 0.25 (45744) hydrogen bonds : bond 0.03757 / 2.45 ( 2640) hydrogen bonds : angle 3.25224 / 2.40 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.450 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.9400 time to fit residues: 492.8694 Evaluate side-chains 456 residues out of total 3600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 235 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 357 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 305 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 269 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.083261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.074152 restraints weight = 38002.602| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.39 r_work: 0.2636 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9345 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34008 Z= 0.179 Angle : 0.444 3.920 45744 Z= 0.248 Chirality : 0.038 0.106 4800 Planarity : 0.003 0.033 5904 Dihedral : 3.875 14.738 4392 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.13), residues: 4032 helix: 3.43 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : 0.92 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 85 TYR 0.011 0.001 TYR W 163 PHE 0.013 0.002 PHE J 39 TRP 0.014 0.002 TRP P 37 HIS 0.003 0.001 HIS G 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (34008) covalent geometry : angle 0.44396 / 0.25 (45744) hydrogen bonds : bond 0.03812 / 2.48 ( 2640) hydrogen bonds : angle 3.25578 / 2.40 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11928.95 seconds wall clock time: 204 minutes 7.00 seconds (12247.00 seconds total)