Starting phenix.real_space_refine on Mon Jul 6 05:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0k_66436/07_2026/9x0k_66436.map" } resolution = 2.19 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= 0.003 sd= 0.020 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 20808 2.51 5 N 5808 2.21 5 O 6744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.04s 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: 33576 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1399 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 164} 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: 3.51, per 1000 atoms: 0.10 Number of scatterers: 33576 At special positions: 0 Unit cell: (127.5, 127.5, 127.5, 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 6744 8.00 N 5808 7.00 C 20808 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: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 11 through 37 Processing helix chain 'A' and resid 46 through 75 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 37 Processing helix chain 'B' and resid 46 through 75 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 37 Processing helix chain 'C' and resid 46 through 75 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 37 Processing helix chain 'D' and resid 46 through 75 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 37 Processing helix chain 'E' and resid 46 through 75 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 37 Processing helix chain 'F' and resid 46 through 75 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 37 Processing helix chain 'G' and resid 46 through 75 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 37 Processing helix chain 'H' and resid 46 through 75 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 37 Processing helix chain 'I' and resid 46 through 75 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 37 Processing helix chain 'J' and resid 46 through 75 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 37 Processing helix chain 'K' and resid 46 through 75 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 37 Processing helix chain 'L' and resid 46 through 75 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 37 Processing helix chain 'M' and resid 46 through 75 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 37 Processing helix chain 'N' and resid 46 through 75 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 37 Processing helix chain 'O' and resid 46 through 75 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 37 Processing helix chain 'P' and resid 46 through 75 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 37 Processing helix chain 'Q' and resid 46 through 75 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 37 Processing helix chain 'R' and resid 46 through 75 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 37 Processing helix chain 'S' and resid 46 through 75 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 37 Processing helix chain 'T' and resid 46 through 75 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 37 Processing helix chain 'V' and resid 46 through 75 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 37 Processing helix chain 'W' and resid 46 through 75 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 37 Processing helix chain 'X' and resid 46 through 75 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 37 Processing helix chain 'Y' and resid 46 through 75 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 2616 hydrogen bonds defined for protein. 7848 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: 5.92 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6120 1.30 - 1.43: 8712 1.43 - 1.56: 18960 1.56 - 1.68: 0 1.68 - 1.81: 408 Bond restraints: 34200 Sorted by residual: bond pdb=" C ALA G 36 " pdb=" N TYR G 37 " ideal model delta sigma weight residual 1.331 1.213 0.118 1.43e-02 4.89e+03 6.83e+01 bond pdb=" C ALA N 36 " pdb=" N TYR N 37 " ideal model delta sigma weight residual 1.331 1.213 0.118 1.43e-02 4.89e+03 6.83e+01 bond pdb=" C ALA T 36 " pdb=" N TYR T 37 " ideal model delta sigma weight residual 1.331 1.213 0.118 1.43e-02 4.89e+03 6.83e+01 bond pdb=" C ALA W 36 " pdb=" N TYR W 37 " ideal model delta sigma weight residual 1.331 1.213 0.118 1.43e-02 4.89e+03 6.83e+01 bond pdb=" C ALA B 36 " pdb=" N TYR B 37 " ideal model delta sigma weight residual 1.331 1.213 0.118 1.43e-02 4.89e+03 6.83e+01 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 28896 1.46 - 2.92: 13488 2.92 - 4.38: 3096 4.38 - 5.84: 432 5.84 - 7.30: 168 Bond angle restraints: 46080 Sorted by residual: angle pdb=" N ASP H 40 " pdb=" CA ASP H 40 " pdb=" C ASP H 40 " ideal model delta sigma weight residual 113.38 107.42 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N ASP J 40 " pdb=" CA ASP J 40 " pdb=" C ASP J 40 " ideal model delta sigma weight residual 113.38 107.42 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N ASP C 40 " pdb=" CA ASP C 40 " pdb=" C ASP C 40 " ideal model delta sigma weight residual 113.38 107.42 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N ASP I 40 " pdb=" CA ASP I 40 " pdb=" C ASP I 40 " ideal model delta sigma weight residual 113.38 107.42 5.96 1.23e+00 6.61e-01 2.35e+01 angle pdb=" N ASP K 40 " pdb=" CA ASP K 40 " pdb=" C ASP K 40 " ideal model delta sigma weight residual 113.38 107.42 5.96 1.23e+00 6.61e-01 2.35e+01 ... (remaining 46075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 18288 14.55 - 29.09: 1920 29.09 - 43.64: 576 43.64 - 58.18: 216 58.18 - 72.73: 120 Dihedral angle restraints: 21120 sinusoidal: 8952 harmonic: 12168 Sorted by residual: dihedral pdb=" CA ARG B 88 " pdb=" CB ARG B 88 " pdb=" CG ARG B 88 " pdb=" CD ARG B 88 " ideal model delta sinusoidal sigma weight residual -180.00 -122.17 -57.83 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG G 88 " pdb=" CB ARG G 88 " pdb=" CG ARG G 88 " pdb=" CD ARG G 88 " ideal model delta sinusoidal sigma weight residual -180.00 -122.17 -57.83 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ARG A 88 " pdb=" CB ARG A 88 " pdb=" CG ARG A 88 " pdb=" CD ARG A 88 " ideal model delta sinusoidal sigma weight residual -180.00 -122.17 -57.83 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 21117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1776 0.048 - 0.096: 1176 0.096 - 0.144: 1200 0.144 - 0.192: 456 0.192 - 0.240: 144 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA ILE G 18 " pdb=" N ILE G 18 " pdb=" C ILE G 18 " pdb=" CB ILE G 18 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE N 18 " pdb=" N ILE N 18 " pdb=" C ILE N 18 " pdb=" CB ILE N 18 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE T 18 " pdb=" N ILE T 18 " pdb=" C ILE T 18 " pdb=" CB ILE T 18 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4749 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 165 " -0.013 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C TYR R 165 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR R 165 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP R 166 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 165 " -0.013 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C TYR C 165 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR C 165 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 166 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 165 " -0.013 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C TYR P 165 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR P 165 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP P 166 " -0.017 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 14808 2.92 - 3.42: 38688 3.42 - 3.91: 64236 3.91 - 4.41: 78540 4.41 - 4.90: 113292 Nonbonded interactions: 309564 Sorted by model distance: nonbonded pdb=" O CYS J 29 " pdb=" OG SER J 57 " model vdw 2.427 3.040 nonbonded pdb=" O CYS H 29 " pdb=" OG SER H 57 " model vdw 2.427 3.040 nonbonded pdb=" O CYS K 29 " pdb=" OG SER K 57 " model vdw 2.427 3.040 nonbonded pdb=" O CYS R 29 " pdb=" OG SER R 57 " model vdw 2.427 3.040 nonbonded pdb=" O CYS Y 29 " pdb=" OG SER Y 57 " model vdw 2.427 3.040 ... (remaining 309559 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 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 0.118 34200 Z= 0.852 Angle : 1.688 7.297 46080 Z= 1.303 Chirality : 0.096 0.240 4752 Planarity : 0.005 0.028 6192 Dihedral : 15.164 72.729 13296 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % 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: -0.20 (0.12), residues: 4056 helix: 0.48 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -2.31 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 41 TYR 0.021 0.004 TYR B 165 PHE 0.011 0.002 PHE K 53 TRP 0.010 0.002 TRP V 91 HIS 0.004 0.001 HIS J 149 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.85 (34200) covalent geometry : angle 1.68847 / 1.30 (46080) hydrogen bonds : bond 0.16506 / 11.03 ( 2616) hydrogen bonds : angle 6.54797 / 4.82 ( 7848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1032 time to evaluate : 1.420 Fit side-chains REVERT: A 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: A 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: A 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7106 (tp40) REVERT: A 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 103 SER cc_start: 0.8420 (t) cc_final: 0.8217 (m) REVERT: A 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: B 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: B 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: B 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: B 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7655 (mt-10) REVERT: B 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: B 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: C 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: C 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: C 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: C 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: C 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: C 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: D 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: D 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: D 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: D 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7657 (mt-10) REVERT: D 103 SER cc_start: 0.8422 (t) cc_final: 0.8220 (m) REVERT: D 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: E 20 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: E 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8120 (ttpp) REVERT: E 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7106 (tp40) REVERT: E 96 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7655 (mt-10) REVERT: E 103 SER cc_start: 0.8421 (t) cc_final: 0.8219 (m) REVERT: E 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: F 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: F 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: F 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7107 (tp40) REVERT: F 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7657 (mt-10) REVERT: F 103 SER cc_start: 0.8423 (t) cc_final: 0.8219 (m) REVERT: F 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: G 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: G 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: G 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7107 (tp40) REVERT: G 96 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7654 (mt-10) REVERT: G 103 SER cc_start: 0.8422 (t) cc_final: 0.8218 (m) REVERT: G 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: H 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: H 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: H 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7107 (tp40) REVERT: H 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7656 (mt-10) REVERT: H 103 SER cc_start: 0.8423 (t) cc_final: 0.8220 (m) REVERT: H 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: I 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: I 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: I 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: I 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: I 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: I 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: J 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: J 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: J 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7107 (tp40) REVERT: J 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7656 (mt-10) REVERT: J 103 SER cc_start: 0.8423 (t) cc_final: 0.8220 (m) REVERT: J 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: K 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: K 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: K 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7107 (tp40) REVERT: K 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7656 (mt-10) REVERT: K 103 SER cc_start: 0.8423 (t) cc_final: 0.8220 (m) REVERT: K 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: L 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: L 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: L 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7106 (tp40) REVERT: L 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: L 103 SER cc_start: 0.8420 (t) cc_final: 0.8217 (m) REVERT: L 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: M 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: M 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: M 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7107 (tp40) REVERT: M 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7657 (mt-10) REVERT: M 103 SER cc_start: 0.8423 (t) cc_final: 0.8219 (m) REVERT: M 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: N 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: N 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: N 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7107 (tp40) REVERT: N 96 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7654 (mt-10) REVERT: N 103 SER cc_start: 0.8422 (t) cc_final: 0.8218 (m) REVERT: N 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: O 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: O 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: O 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7106 (tp40) REVERT: O 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: O 103 SER cc_start: 0.8420 (t) cc_final: 0.8217 (m) REVERT: O 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: P 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: P 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: P 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: P 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: P 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: P 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: Q 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: Q 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: Q 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: Q 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7655 (mt-10) REVERT: Q 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: Q 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: R 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: R 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: R 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: R 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7657 (mt-10) REVERT: R 103 SER cc_start: 0.8422 (t) cc_final: 0.8220 (m) REVERT: R 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: S 20 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: S 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8120 (ttpp) REVERT: S 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7106 (tp40) REVERT: S 96 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7655 (mt-10) REVERT: S 103 SER cc_start: 0.8421 (t) cc_final: 0.8219 (m) REVERT: S 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: T 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: T 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: T 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7107 (tp40) REVERT: T 96 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7654 (mt-10) REVERT: T 103 SER cc_start: 0.8422 (t) cc_final: 0.8218 (m) REVERT: T 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) REVERT: V 20 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: V 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: V 55 GLN cc_start: 0.7960 (tt0) cc_final: 0.7107 (tp40) REVERT: V 96 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7657 (mt-10) REVERT: V 103 SER cc_start: 0.8423 (t) cc_final: 0.8219 (m) REVERT: V 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: W 20 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: W 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8120 (ttpp) REVERT: W 55 GLN cc_start: 0.7959 (tt0) cc_final: 0.7106 (tp40) REVERT: W 96 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7655 (mt-10) REVERT: W 103 SER cc_start: 0.8421 (t) cc_final: 0.8219 (m) REVERT: W 111 SER cc_start: 0.8333 (m) cc_final: 0.8068 (t) REVERT: X 20 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7234 (ttp80) REVERT: X 51 LYS cc_start: 0.8392 (tttp) cc_final: 0.8120 (ttpp) REVERT: X 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: X 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7655 (mt-10) REVERT: X 103 SER cc_start: 0.8422 (t) cc_final: 0.8219 (m) REVERT: X 111 SER cc_start: 0.8334 (m) cc_final: 0.8070 (t) REVERT: Y 20 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7233 (ttp80) REVERT: Y 51 LYS cc_start: 0.8393 (tttp) cc_final: 0.8121 (ttpp) REVERT: Y 55 GLN cc_start: 0.7961 (tt0) cc_final: 0.7108 (tp40) REVERT: Y 96 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7657 (mt-10) REVERT: Y 103 SER cc_start: 0.8422 (t) cc_final: 0.8220 (m) REVERT: Y 111 SER cc_start: 0.8333 (m) cc_final: 0.8069 (t) outliers start: 0 outliers final: 0 residues processed: 1032 average time/residue: 0.9538 time to fit residues: 1119.3044 Evaluate side-chains 744 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 744 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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: 7.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN A 5 GLN B 3 GLN B 5 GLN C 3 GLN C 5 GLN D 3 GLN D 5 GLN E 3 GLN E 5 GLN F 3 GLN F 5 GLN G 3 GLN G 5 GLN H 3 GLN H 5 GLN I 3 GLN I 5 GLN J 3 GLN J 5 GLN K 3 GLN K 5 GLN L 3 GLN L 5 GLN M 3 GLN M 5 GLN N 3 GLN N 5 GLN O 3 GLN O 5 GLN P 3 GLN P 5 GLN Q 3 GLN Q 5 GLN R 3 GLN R 5 GLN S 3 GLN S 5 GLN T 3 GLN T 5 GLN V 3 GLN V 5 GLN W 3 GLN W 5 GLN X 3 GLN X 5 GLN Y 3 GLN Y 5 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.080394 restraints weight = 38971.513| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.43 r_work: 0.2756 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9406 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34200 Z= 0.172 Angle : 0.517 4.818 46080 Z= 0.284 Chirality : 0.040 0.123 4752 Planarity : 0.004 0.020 6192 Dihedral : 6.265 65.061 4584 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.32 % Allowed : 9.21 % Favored : 89.47 % 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: 3.36 (0.12), residues: 4056 helix: 3.07 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.30 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG X 61 TYR 0.020 0.002 TYR P 37 PHE 0.006 0.002 PHE G 49 TRP 0.003 0.001 TRP A 91 HIS 0.002 0.001 HIS W 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (34200) covalent geometry : angle 0.51670 / 0.28 (46080) hydrogen bonds : bond 0.04165 / 2.80 ( 2616) hydrogen bonds : angle 3.60948 / 2.66 ( 7848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 720 time to evaluate : 1.455 Fit side-chains REVERT: A 20 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: A 55 GLN cc_start: 0.8822 (tt0) cc_final: 0.8254 (tp-100) REVERT: A 96 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8508 (mt-10) REVERT: B 20 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8267 (ttp80) REVERT: B 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8252 (tp-100) REVERT: B 96 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8516 (mt-10) REVERT: C 20 ARG cc_start: 0.8555 (ttp-110) cc_final: 0.8267 (ttp80) REVERT: C 55 GLN cc_start: 0.8817 (tt0) cc_final: 0.8250 (tp-100) REVERT: C 96 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8515 (mt-10) REVERT: D 20 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: D 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8244 (tp-100) REVERT: D 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8519 (mt-10) REVERT: E 20 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: E 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8255 (tp-100) REVERT: E 96 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8506 (mt-10) REVERT: F 20 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8271 (ttp80) REVERT: F 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8253 (tp-100) REVERT: F 96 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8516 (mt-10) REVERT: G 20 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8272 (ttp80) REVERT: G 55 GLN cc_start: 0.8824 (tt0) cc_final: 0.8257 (tp-100) REVERT: G 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8517 (mt-10) REVERT: H 20 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8260 (ttp80) REVERT: H 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8249 (tp-100) REVERT: H 96 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8512 (mt-10) REVERT: I 20 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8268 (ttp80) REVERT: I 55 GLN cc_start: 0.8818 (tt0) cc_final: 0.8251 (tp-100) REVERT: I 96 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8515 (mt-10) REVERT: J 20 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8260 (ttp80) REVERT: J 55 GLN cc_start: 0.8814 (tt0) cc_final: 0.8249 (tp-100) REVERT: J 96 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8511 (mt-10) REVERT: K 20 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8260 (ttp80) REVERT: K 55 GLN cc_start: 0.8812 (tt0) cc_final: 0.8247 (tp-100) REVERT: K 96 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8513 (mt-10) REVERT: L 20 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: L 55 GLN cc_start: 0.8821 (tt0) cc_final: 0.8253 (tp-100) REVERT: L 96 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8510 (mt-10) REVERT: M 20 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8271 (ttp80) REVERT: M 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8252 (tp-100) REVERT: M 96 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8517 (mt-10) REVERT: N 20 ARG cc_start: 0.8548 (ttp-110) cc_final: 0.8272 (ttp80) REVERT: N 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8258 (tp-100) REVERT: N 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8516 (mt-10) REVERT: O 20 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: O 55 GLN cc_start: 0.8822 (tt0) cc_final: 0.8254 (tp-100) REVERT: O 96 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8509 (mt-10) REVERT: P 20 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8268 (ttp80) REVERT: P 55 GLN cc_start: 0.8818 (tt0) cc_final: 0.8251 (tp-100) REVERT: P 96 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8516 (mt-10) REVERT: Q 20 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8267 (ttp80) REVERT: Q 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8253 (tp-100) REVERT: Q 96 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8515 (mt-10) REVERT: R 20 ARG cc_start: 0.8543 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: R 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8244 (tp-100) REVERT: R 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8519 (mt-10) REVERT: S 20 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8268 (ttp80) REVERT: S 55 GLN cc_start: 0.8809 (tt0) cc_final: 0.8254 (tp-100) REVERT: S 96 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8505 (mt-10) REVERT: T 20 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8272 (ttp80) REVERT: T 55 GLN cc_start: 0.8826 (tt0) cc_final: 0.8259 (tp-100) REVERT: T 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8516 (mt-10) REVERT: V 20 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8271 (ttp80) REVERT: V 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8253 (tp-100) REVERT: V 96 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8516 (mt-10) REVERT: W 20 ARG cc_start: 0.8551 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: W 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8255 (tp-100) REVERT: W 96 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8506 (mt-10) REVERT: X 20 ARG cc_start: 0.8549 (ttp-110) cc_final: 0.8267 (ttp80) REVERT: X 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8252 (tp-100) REVERT: X 96 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8515 (mt-10) REVERT: Y 20 ARG cc_start: 0.8544 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: Y 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8245 (tp-100) REVERT: Y 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8518 (mt-10) outliers start: 48 outliers final: 0 residues processed: 744 average time/residue: 1.0114 time to fit residues: 850.6239 Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 130 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 398 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN B 21 GLN C 21 GLN D 21 GLN E 21 GLN F 21 GLN G 21 GLN H 21 GLN I 21 GLN J 21 GLN K 21 GLN L 21 GLN M 21 GLN N 21 GLN O 21 GLN P 21 GLN Q 21 GLN R 21 GLN S 21 GLN T 21 GLN V 21 GLN W 21 GLN X 21 GLN Y 21 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.087639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.077952 restraints weight = 39125.444| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.48 r_work: 0.2664 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9432 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34200 Z= 0.193 Angle : 0.503 4.766 46080 Z= 0.275 Chirality : 0.040 0.129 4752 Planarity : 0.004 0.025 6192 Dihedral : 6.120 62.816 4584 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.66 % Allowed : 11.18 % Favored : 88.16 % 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: 3.99 (0.12), residues: 4056 helix: 3.51 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.37 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 61 TYR 0.023 0.002 TYR E 37 PHE 0.007 0.002 PHE Q 53 TRP 0.006 0.002 TRP A 91 HIS 0.002 0.001 HIS G 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (34200) covalent geometry : angle 0.50254 / 0.28 (46080) hydrogen bonds : bond 0.04146 / 2.79 ( 2616) hydrogen bonds : angle 3.55969 / 2.63 ( 7848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 528 time to evaluate : 1.418 Fit side-chains REVERT: A 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8318 (ttp80) REVERT: A 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8311 (tp-100) REVERT: A 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8508 (mt-10) REVERT: B 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: B 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8314 (tp-100) REVERT: B 96 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8516 (mt-10) REVERT: C 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8315 (ttp80) REVERT: C 55 GLN cc_start: 0.8823 (tt0) cc_final: 0.8311 (tp-100) REVERT: C 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8503 (mt-10) REVERT: D 20 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8323 (ttp80) REVERT: D 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8305 (tp-100) REVERT: D 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8510 (mt-10) REVERT: E 20 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: E 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8312 (tp-100) REVERT: E 96 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8512 (mt-10) REVERT: F 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8326 (ttp80) REVERT: F 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8309 (tp-100) REVERT: F 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8514 (mt-10) REVERT: G 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: G 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8312 (tp-100) REVERT: G 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8511 (mt-10) REVERT: H 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: H 55 GLN cc_start: 0.8817 (tt0) cc_final: 0.8309 (tp-100) REVERT: H 96 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8514 (mt-10) REVERT: I 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8315 (ttp80) REVERT: I 55 GLN cc_start: 0.8823 (tt0) cc_final: 0.8311 (tp-100) REVERT: I 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8503 (mt-10) REVERT: J 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: J 55 GLN cc_start: 0.8817 (tt0) cc_final: 0.8309 (tp-100) REVERT: J 96 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8514 (mt-10) REVERT: K 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: K 55 GLN cc_start: 0.8817 (tt0) cc_final: 0.8309 (tp-100) REVERT: K 96 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8514 (mt-10) REVERT: L 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8318 (ttp80) REVERT: L 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8311 (tp-100) REVERT: L 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8508 (mt-10) REVERT: M 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8325 (ttp80) REVERT: M 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8309 (tp-100) REVERT: M 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8514 (mt-10) REVERT: N 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: N 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8312 (tp-100) REVERT: N 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8511 (mt-10) REVERT: O 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8318 (ttp80) REVERT: O 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8311 (tp-100) REVERT: O 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8508 (mt-10) REVERT: P 20 ARG cc_start: 0.8588 (ttp-110) cc_final: 0.8315 (ttp80) REVERT: P 55 GLN cc_start: 0.8823 (tt0) cc_final: 0.8311 (tp-100) REVERT: P 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8503 (mt-10) REVERT: Q 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: Q 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8314 (tp-100) REVERT: Q 96 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8516 (mt-10) REVERT: R 20 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8323 (ttp80) REVERT: R 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8305 (tp-100) REVERT: R 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8510 (mt-10) REVERT: S 20 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8321 (ttp80) REVERT: S 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8312 (tp-100) REVERT: S 96 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8512 (mt-10) REVERT: T 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8322 (ttp80) REVERT: T 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8312 (tp-100) REVERT: T 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8511 (mt-10) REVERT: V 20 ARG cc_start: 0.8605 (ttp-110) cc_final: 0.8325 (ttp80) REVERT: V 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8309 (tp-100) REVERT: V 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8514 (mt-10) REVERT: W 20 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: W 55 GLN cc_start: 0.8815 (tt0) cc_final: 0.8312 (tp-100) REVERT: W 96 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8512 (mt-10) REVERT: X 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8320 (ttp80) REVERT: X 55 GLN cc_start: 0.8820 (tt0) cc_final: 0.8314 (tp-100) REVERT: X 96 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8516 (mt-10) REVERT: Y 20 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8323 (ttp80) REVERT: Y 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8305 (tp-100) REVERT: Y 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8510 (mt-10) outliers start: 24 outliers final: 0 residues processed: 528 average time/residue: 1.0095 time to fit residues: 606.0341 Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 270 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 367 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 372 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.2949 r_free = 0.2949 target = 0.086261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.076792 restraints weight = 39349.665| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.47 r_work: 0.2643 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9441 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34200 Z= 0.213 Angle : 0.501 4.840 46080 Z= 0.275 Chirality : 0.040 0.134 4752 Planarity : 0.004 0.026 6192 Dihedral : 5.998 60.593 4584 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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: 4.17 (0.12), residues: 4056 helix: 3.64 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.34 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 61 TYR 0.024 0.002 TYR E 37 PHE 0.008 0.002 PHE Q 53 TRP 0.006 0.002 TRP A 91 HIS 0.003 0.001 HIS T 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (34200) covalent geometry : angle 0.50123 / 0.28 (46080) hydrogen bonds : bond 0.04228 / 2.85 ( 2616) hydrogen bonds : angle 3.56375 / 2.63 ( 7848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.528 Fit side-chains REVERT: A 20 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: A 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8347 (tp-100) REVERT: A 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 20 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: B 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8352 (tp-100) REVERT: B 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 20 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: C 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8350 (tp-100) REVERT: C 96 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8480 (mt-10) REVERT: D 20 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: D 55 GLN cc_start: 0.8813 (tt0) cc_final: 0.8342 (tp-100) REVERT: D 96 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8481 (mt-10) REVERT: E 20 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: E 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: E 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8479 (mt-10) REVERT: F 20 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8357 (ttp80) REVERT: F 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8341 (tp-100) REVERT: F 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8488 (mt-10) REVERT: G 20 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: G 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: G 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8482 (mt-10) REVERT: H 20 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8346 (ttp80) REVERT: H 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8348 (tp-100) REVERT: H 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8483 (mt-10) REVERT: I 20 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: I 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8350 (tp-100) REVERT: I 96 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8480 (mt-10) REVERT: J 20 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8346 (ttp80) REVERT: J 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8348 (tp-100) REVERT: J 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8483 (mt-10) REVERT: K 20 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8346 (ttp80) REVERT: K 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8348 (tp-100) REVERT: K 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8483 (mt-10) REVERT: L 20 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: L 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8347 (tp-100) REVERT: L 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8481 (mt-10) REVERT: M 20 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8357 (ttp80) REVERT: M 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8341 (tp-100) REVERT: M 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8488 (mt-10) REVERT: N 20 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: N 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: N 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8482 (mt-10) REVERT: O 20 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: O 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8347 (tp-100) REVERT: O 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8481 (mt-10) REVERT: P 20 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: P 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8350 (tp-100) REVERT: P 96 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8480 (mt-10) REVERT: Q 20 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: Q 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8353 (tp-100) REVERT: Q 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: R 20 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: R 55 GLN cc_start: 0.8813 (tt0) cc_final: 0.8342 (tp-100) REVERT: R 96 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8481 (mt-10) REVERT: S 20 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: S 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: S 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8479 (mt-10) REVERT: T 20 ARG cc_start: 0.8647 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: T 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: T 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8482 (mt-10) REVERT: V 20 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8357 (ttp80) REVERT: V 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8341 (tp-100) REVERT: V 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8488 (mt-10) REVERT: W 20 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: W 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8346 (tp-100) REVERT: W 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8479 (mt-10) REVERT: X 20 ARG cc_start: 0.8644 (ttp-110) cc_final: 0.8353 (ttp80) REVERT: X 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8352 (tp-100) REVERT: X 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: Y 20 ARG cc_start: 0.8641 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: Y 55 GLN cc_start: 0.8813 (tt0) cc_final: 0.8342 (tp-100) REVERT: Y 96 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8481 (mt-10) outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 1.0272 time to fit residues: 644.4916 Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 200 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 323 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 170 optimal weight: 0.0570 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 overall best weight: 3.8102 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.088330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.078907 restraints weight = 39266.703| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.47 r_work: 0.2680 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9417 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34200 Z= 0.135 Angle : 0.436 4.535 46080 Z= 0.241 Chirality : 0.037 0.126 4752 Planarity : 0.003 0.026 6192 Dihedral : 5.710 57.032 4584 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.66 % Allowed : 10.53 % Favored : 88.82 % 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: 4056 helix: 4.04 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.94 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 61 TYR 0.019 0.002 TYR E 37 PHE 0.005 0.001 PHE M 53 TRP 0.006 0.001 TRP A 91 HIS 0.002 0.001 HIS R 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (34200) covalent geometry : angle 0.43610 / 0.24 (46080) hydrogen bonds : bond 0.03593 / 2.42 ( 2616) hydrogen bonds : angle 3.43444 / 2.53 ( 7848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 552 time to evaluate : 1.372 Fit side-chains REVERT: A 20 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: A 55 GLN cc_start: 0.8792 (tt0) cc_final: 0.8338 (tp-100) REVERT: A 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 20 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: B 55 GLN cc_start: 0.8796 (tt0) cc_final: 0.8339 (tp-100) REVERT: B 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8501 (mt-10) REVERT: C 20 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: C 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8340 (tp-100) REVERT: C 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8497 (mt-10) REVERT: D 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8273 (ttp80) REVERT: D 55 GLN cc_start: 0.8785 (tt0) cc_final: 0.8332 (tp-100) REVERT: D 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8489 (mt-10) REVERT: E 20 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8262 (ttp80) REVERT: E 55 GLN cc_start: 0.8790 (tt0) cc_final: 0.8338 (tp-100) REVERT: E 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8491 (mt-10) REVERT: F 20 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: F 55 GLN cc_start: 0.8781 (tt0) cc_final: 0.8326 (tp-100) REVERT: F 96 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8506 (mt-10) REVERT: G 20 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: G 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8339 (tp-100) REVERT: G 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8496 (mt-10) REVERT: H 20 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: H 55 GLN cc_start: 0.8788 (tt0) cc_final: 0.8335 (tp-100) REVERT: H 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8489 (mt-10) REVERT: I 20 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: I 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8340 (tp-100) REVERT: I 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8497 (mt-10) REVERT: J 20 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: J 55 GLN cc_start: 0.8788 (tt0) cc_final: 0.8335 (tp-100) REVERT: J 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8488 (mt-10) REVERT: K 20 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: K 55 GLN cc_start: 0.8788 (tt0) cc_final: 0.8335 (tp-100) REVERT: K 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8489 (mt-10) REVERT: L 20 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: L 55 GLN cc_start: 0.8792 (tt0) cc_final: 0.8338 (tp-100) REVERT: L 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8490 (mt-10) REVERT: M 20 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: M 55 GLN cc_start: 0.8781 (tt0) cc_final: 0.8326 (tp-100) REVERT: M 96 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8506 (mt-10) REVERT: N 20 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: N 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8339 (tp-100) REVERT: N 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8497 (mt-10) REVERT: O 20 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8264 (ttp80) REVERT: O 55 GLN cc_start: 0.8792 (tt0) cc_final: 0.8338 (tp-100) REVERT: O 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8490 (mt-10) REVERT: P 20 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: P 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8339 (tp-100) REVERT: P 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8497 (mt-10) REVERT: Q 20 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: Q 55 GLN cc_start: 0.8796 (tt0) cc_final: 0.8339 (tp-100) REVERT: Q 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8501 (mt-10) REVERT: R 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8273 (ttp80) REVERT: R 55 GLN cc_start: 0.8784 (tt0) cc_final: 0.8332 (tp-100) REVERT: R 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8489 (mt-10) REVERT: S 20 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8262 (ttp80) REVERT: S 55 GLN cc_start: 0.8790 (tt0) cc_final: 0.8338 (tp-100) REVERT: S 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8491 (mt-10) REVERT: T 20 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: T 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8339 (tp-100) REVERT: T 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8497 (mt-10) REVERT: V 20 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8268 (ttp80) REVERT: V 55 GLN cc_start: 0.8781 (tt0) cc_final: 0.8326 (tp-100) REVERT: V 96 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8506 (mt-10) REVERT: W 20 ARG cc_start: 0.8583 (ttp-110) cc_final: 0.8262 (ttp80) REVERT: W 55 GLN cc_start: 0.8790 (tt0) cc_final: 0.8338 (tp-100) REVERT: W 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8491 (mt-10) REVERT: X 20 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8265 (ttp80) REVERT: X 55 GLN cc_start: 0.8796 (tt0) cc_final: 0.8339 (tp-100) REVERT: X 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8501 (mt-10) REVERT: Y 20 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8273 (ttp80) REVERT: Y 55 GLN cc_start: 0.8785 (tt0) cc_final: 0.8332 (tp-100) REVERT: Y 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8489 (mt-10) outliers start: 24 outliers final: 0 residues processed: 552 average time/residue: 0.9727 time to fit residues: 612.3307 Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 88 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 350 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 317 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 overall best weight: 9.7990 ------------------------------------------------------------------------------- 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 = 0.2934 r_free = 0.2934 target = 0.085463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.076065 restraints weight = 39346.450| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.46 r_work: 0.2630 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9447 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 34200 Z= 0.252 Angle : 0.513 5.096 46080 Z= 0.282 Chirality : 0.042 0.138 4752 Planarity : 0.004 0.029 6192 Dihedral : 5.760 56.346 4584 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % 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: 4.28 (0.13), residues: 4056 helix: 3.70 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 77 TYR 0.022 0.002 TYR O 37 PHE 0.009 0.002 PHE J 53 TRP 0.006 0.002 TRP L 91 HIS 0.003 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (34200) covalent geometry : angle 0.51285 / 0.28 (46080) hydrogen bonds : bond 0.04366 / 2.94 ( 2616) hydrogen bonds : angle 3.56838 / 2.64 ( 7848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.489 Fit side-chains REVERT: A 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8363 (ttp80) REVERT: A 55 GLN cc_start: 0.8830 (tt0) cc_final: 0.8367 (tp-100) REVERT: A 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8485 (mt-10) REVERT: B 20 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: B 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8373 (tp-100) REVERT: B 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8490 (mt-10) REVERT: C 20 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: C 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8369 (tp-100) REVERT: C 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8486 (mt-10) REVERT: D 20 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: D 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8369 (tp-100) REVERT: D 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8479 (mt-10) REVERT: E 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8360 (ttp80) REVERT: E 55 GLN cc_start: 0.8832 (tt0) cc_final: 0.8369 (tp-100) REVERT: E 96 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8479 (mt-10) REVERT: F 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: F 55 GLN cc_start: 0.8824 (tt0) cc_final: 0.8363 (tp-100) REVERT: F 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8492 (mt-10) REVERT: G 20 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8365 (ttp80) REVERT: G 55 GLN cc_start: 0.8838 (tt0) cc_final: 0.8371 (tp-100) REVERT: G 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8489 (mt-10) REVERT: H 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: H 55 GLN cc_start: 0.8828 (tt0) cc_final: 0.8371 (tp-100) REVERT: H 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8483 (mt-10) REVERT: I 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: I 55 GLN cc_start: 0.8833 (tt0) cc_final: 0.8369 (tp-100) REVERT: I 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8486 (mt-10) REVERT: J 20 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: J 55 GLN cc_start: 0.8829 (tt0) cc_final: 0.8372 (tp-100) REVERT: J 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8483 (mt-10) REVERT: K 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: K 55 GLN cc_start: 0.8828 (tt0) cc_final: 0.8372 (tp-100) REVERT: K 96 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8482 (mt-10) REVERT: L 20 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8363 (ttp80) REVERT: L 55 GLN cc_start: 0.8830 (tt0) cc_final: 0.8367 (tp-100) REVERT: L 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8484 (mt-10) REVERT: M 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: M 55 GLN cc_start: 0.8824 (tt0) cc_final: 0.8362 (tp-100) REVERT: M 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8492 (mt-10) REVERT: N 20 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8365 (ttp80) REVERT: N 55 GLN cc_start: 0.8838 (tt0) cc_final: 0.8371 (tp-100) REVERT: N 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8488 (mt-10) REVERT: O 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8363 (ttp80) REVERT: O 55 GLN cc_start: 0.8830 (tt0) cc_final: 0.8367 (tp-100) REVERT: O 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8485 (mt-10) REVERT: P 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8359 (ttp80) REVERT: P 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8369 (tp-100) REVERT: P 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8486 (mt-10) REVERT: Q 20 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8360 (ttp80) REVERT: Q 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8373 (tp-100) REVERT: Q 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8490 (mt-10) REVERT: R 20 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: R 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8369 (tp-100) REVERT: R 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8479 (mt-10) REVERT: S 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8361 (ttp80) REVERT: S 55 GLN cc_start: 0.8832 (tt0) cc_final: 0.8369 (tp-100) REVERT: S 96 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8479 (mt-10) REVERT: T 20 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8365 (ttp80) REVERT: T 55 GLN cc_start: 0.8838 (tt0) cc_final: 0.8371 (tp-100) REVERT: T 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8489 (mt-10) REVERT: V 20 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: V 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8363 (tp-100) REVERT: V 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8492 (mt-10) REVERT: W 20 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8360 (ttp80) REVERT: W 55 GLN cc_start: 0.8832 (tt0) cc_final: 0.8369 (tp-100) REVERT: W 96 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8479 (mt-10) REVERT: X 20 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8360 (ttp80) REVERT: X 55 GLN cc_start: 0.8833 (tt0) cc_final: 0.8372 (tp-100) REVERT: X 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8490 (mt-10) REVERT: Y 20 ARG cc_start: 0.8663 (ttp-110) cc_final: 0.8362 (ttp80) REVERT: Y 55 GLN cc_start: 0.8825 (tt0) cc_final: 0.8369 (tp-100) REVERT: Y 96 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8479 (mt-10) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.8705 time to fit residues: 479.6999 Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 9.9990 chunk 340 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 187 optimal weight: 0.0770 chunk 89 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 4.1744 ------------------------------------------------------------------------------- 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 = 0.2976 r_free = 0.2976 target = 0.087978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.078555 restraints weight = 39272.356| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.47 r_work: 0.2674 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9421 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34200 Z= 0.140 Angle : 0.437 4.510 46080 Z= 0.242 Chirality : 0.037 0.128 4752 Planarity : 0.003 0.028 6192 Dihedral : 5.470 52.373 4584 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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: 4.58 (0.13), residues: 4056 helix: 3.92 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 61 TYR 0.019 0.002 TYR X 37 PHE 0.006 0.001 PHE J 53 TRP 0.006 0.001 TRP J 91 HIS 0.002 0.001 HIS T 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (34200) covalent geometry : angle 0.43721 / 0.24 (46080) hydrogen bonds : bond 0.03634 / 2.44 ( 2616) hydrogen bonds : angle 3.43064 / 2.53 ( 7848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.537 Fit side-chains REVERT: A 20 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8284 (ttp80) REVERT: A 55 GLN cc_start: 0.8797 (tt0) cc_final: 0.8342 (tp-100) REVERT: A 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8494 (mt-10) REVERT: B 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: B 55 GLN cc_start: 0.8808 (tt0) cc_final: 0.8349 (tp-100) REVERT: B 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8497 (mt-10) REVERT: C 20 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8286 (ttp80) REVERT: C 55 GLN cc_start: 0.8809 (tt0) cc_final: 0.8348 (tp-100) REVERT: C 96 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8502 (mt-10) REVERT: D 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8291 (ttp80) REVERT: D 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8341 (tp-100) REVERT: D 96 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8489 (mt-10) REVERT: E 20 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8282 (ttp80) REVERT: E 55 GLN cc_start: 0.8803 (tt0) cc_final: 0.8347 (tp-100) REVERT: E 96 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8494 (mt-10) REVERT: F 20 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8292 (ttp80) REVERT: F 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8334 (tp-100) REVERT: F 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8506 (mt-10) REVERT: G 20 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: G 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8345 (tp-100) REVERT: G 96 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8499 (mt-10) REVERT: H 20 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8281 (ttp80) REVERT: H 55 GLN cc_start: 0.8797 (tt0) cc_final: 0.8342 (tp-100) REVERT: H 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8498 (mt-10) REVERT: I 20 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8286 (ttp80) REVERT: I 55 GLN cc_start: 0.8809 (tt0) cc_final: 0.8348 (tp-100) REVERT: I 96 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8502 (mt-10) REVERT: J 20 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8281 (ttp80) REVERT: J 55 GLN cc_start: 0.8797 (tt0) cc_final: 0.8341 (tp-100) REVERT: J 96 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8498 (mt-10) REVERT: K 20 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8281 (ttp80) REVERT: K 55 GLN cc_start: 0.8797 (tt0) cc_final: 0.8342 (tp-100) REVERT: K 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8499 (mt-10) REVERT: L 20 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8283 (ttp80) REVERT: L 55 GLN cc_start: 0.8797 (tt0) cc_final: 0.8342 (tp-100) REVERT: L 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8493 (mt-10) REVERT: M 20 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8292 (ttp80) REVERT: M 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8334 (tp-100) REVERT: M 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8506 (mt-10) REVERT: N 20 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: N 55 GLN cc_start: 0.8806 (tt0) cc_final: 0.8345 (tp-100) REVERT: N 96 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8499 (mt-10) REVERT: O 20 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8284 (ttp80) REVERT: O 55 GLN cc_start: 0.8796 (tt0) cc_final: 0.8341 (tp-100) REVERT: O 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8494 (mt-10) REVERT: P 20 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8286 (ttp80) REVERT: P 55 GLN cc_start: 0.8808 (tt0) cc_final: 0.8348 (tp-100) REVERT: P 96 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8502 (mt-10) REVERT: Q 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: Q 55 GLN cc_start: 0.8808 (tt0) cc_final: 0.8349 (tp-100) REVERT: Q 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8497 (mt-10) REVERT: R 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8291 (ttp80) REVERT: R 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8341 (tp-100) REVERT: R 96 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8489 (mt-10) REVERT: S 20 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8282 (ttp80) REVERT: S 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8347 (tp-100) REVERT: S 96 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8494 (mt-10) REVERT: T 20 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: T 55 GLN cc_start: 0.8806 (tt0) cc_final: 0.8345 (tp-100) REVERT: T 96 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8499 (mt-10) REVERT: V 20 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8292 (ttp80) REVERT: V 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8334 (tp-100) REVERT: V 96 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8506 (mt-10) REVERT: W 20 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8282 (ttp80) REVERT: W 55 GLN cc_start: 0.8803 (tt0) cc_final: 0.8348 (tp-100) REVERT: W 96 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8494 (mt-10) REVERT: X 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8290 (ttp80) REVERT: X 55 GLN cc_start: 0.8808 (tt0) cc_final: 0.8349 (tp-100) REVERT: X 96 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8497 (mt-10) REVERT: Y 20 ARG cc_start: 0.8608 (ttp-110) cc_final: 0.8291 (ttp80) REVERT: Y 55 GLN cc_start: 0.8786 (tt0) cc_final: 0.8341 (tp-100) REVERT: Y 96 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8489 (mt-10) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.9159 time to fit residues: 526.0342 Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 352 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 356 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.086855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.077477 restraints weight = 39297.568| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.46 r_work: 0.2655 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9432 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34200 Z= 0.174 Angle : 0.460 4.634 46080 Z= 0.254 Chirality : 0.039 0.130 4752 Planarity : 0.004 0.029 6192 Dihedral : 5.341 49.218 4584 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % 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: 4056 helix: 3.85 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.14 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 77 TYR 0.019 0.002 TYR X 37 PHE 0.007 0.001 PHE Y 53 TRP 0.006 0.002 TRP D 91 HIS 0.002 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (34200) covalent geometry : angle 0.46043 / 0.25 (46080) hydrogen bonds : bond 0.03905 / 2.63 ( 2616) hydrogen bonds : angle 3.47511 / 2.57 ( 7848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.382 Fit side-chains REVERT: A 20 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: A 55 GLN cc_start: 0.8803 (tt0) cc_final: 0.8348 (tp-100) REVERT: A 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8490 (mt-10) REVERT: B 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: B 55 GLN cc_start: 0.8818 (tt0) cc_final: 0.8363 (tp-100) REVERT: B 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: C 20 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: C 55 GLN cc_start: 0.8812 (tt0) cc_final: 0.8356 (tp-100) REVERT: C 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8494 (mt-10) REVERT: D 20 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: D 55 GLN cc_start: 0.8788 (tt0) cc_final: 0.8351 (tp-100) REVERT: D 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8488 (mt-10) REVERT: E 20 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8303 (ttp80) REVERT: E 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8353 (tp-100) REVERT: E 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8484 (mt-10) REVERT: F 20 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8307 (ttp80) REVERT: F 55 GLN cc_start: 0.8794 (tt0) cc_final: 0.8346 (tp-100) REVERT: F 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8498 (mt-10) REVERT: G 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8312 (ttp80) REVERT: G 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8356 (tp-100) REVERT: G 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8486 (mt-10) REVERT: H 20 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8302 (ttp80) REVERT: H 55 GLN cc_start: 0.8796 (tt0) cc_final: 0.8352 (tp-100) REVERT: H 96 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8491 (mt-10) REVERT: I 20 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: I 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8356 (tp-100) REVERT: I 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8495 (mt-10) REVERT: J 20 ARG cc_start: 0.8614 (ttp-110) cc_final: 0.8302 (ttp80) REVERT: J 55 GLN cc_start: 0.8798 (tt0) cc_final: 0.8352 (tp-100) REVERT: J 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8492 (mt-10) REVERT: K 20 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8302 (ttp80) REVERT: K 55 GLN cc_start: 0.8798 (tt0) cc_final: 0.8352 (tp-100) REVERT: K 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8491 (mt-10) REVERT: L 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: L 55 GLN cc_start: 0.8803 (tt0) cc_final: 0.8348 (tp-100) REVERT: L 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8491 (mt-10) REVERT: M 20 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8308 (ttp80) REVERT: M 55 GLN cc_start: 0.8795 (tt0) cc_final: 0.8346 (tp-100) REVERT: M 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8498 (mt-10) REVERT: N 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8312 (ttp80) REVERT: N 55 GLN cc_start: 0.8809 (tt0) cc_final: 0.8357 (tp-100) REVERT: N 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8485 (mt-10) REVERT: O 20 ARG cc_start: 0.8623 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: O 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8348 (tp-100) REVERT: O 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8491 (mt-10) REVERT: P 20 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: P 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8356 (tp-100) REVERT: P 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8494 (mt-10) REVERT: Q 20 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: Q 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8362 (tp-100) REVERT: Q 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: R 20 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: R 55 GLN cc_start: 0.8788 (tt0) cc_final: 0.8352 (tp-100) REVERT: R 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8488 (mt-10) REVERT: S 20 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8303 (ttp80) REVERT: S 55 GLN cc_start: 0.8804 (tt0) cc_final: 0.8353 (tp-100) REVERT: S 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8484 (mt-10) REVERT: T 20 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8312 (ttp80) REVERT: T 55 GLN cc_start: 0.8807 (tt0) cc_final: 0.8355 (tp-100) REVERT: T 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8485 (mt-10) REVERT: V 20 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8308 (ttp80) REVERT: V 55 GLN cc_start: 0.8794 (tt0) cc_final: 0.8346 (tp-100) REVERT: V 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8498 (mt-10) REVERT: W 20 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8302 (ttp80) REVERT: W 55 GLN cc_start: 0.8805 (tt0) cc_final: 0.8354 (tp-100) REVERT: W 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8484 (mt-10) REVERT: X 20 ARG cc_start: 0.8630 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: X 55 GLN cc_start: 0.8817 (tt0) cc_final: 0.8362 (tp-100) REVERT: X 96 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8489 (mt-10) REVERT: Y 20 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.8304 (ttp80) REVERT: Y 55 GLN cc_start: 0.8789 (tt0) cc_final: 0.8352 (tp-100) REVERT: Y 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8488 (mt-10) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.9127 time to fit residues: 502.2230 Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 324 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 8 optimal weight: 30.0000 chunk 312 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.086005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.076561 restraints weight = 39038.276| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 1.45 r_work: 0.2638 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9442 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 34200 Z= 0.219 Angle : 0.493 4.885 46080 Z= 0.271 Chirality : 0.040 0.134 4752 Planarity : 0.004 0.030 6192 Dihedral : 5.332 48.205 4584 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % 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 (0.13), residues: 4056 helix: 3.74 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.11 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 77 TYR 0.022 0.002 TYR D 37 PHE 0.009 0.002 PHE K 53 TRP 0.006 0.002 TRP A 91 HIS 0.003 0.001 HIS T 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (34200) covalent geometry : angle 0.49282 / 0.27 (46080) hydrogen bonds : bond 0.04189 / 2.82 ( 2616) hydrogen bonds : angle 3.52915 / 2.61 ( 7848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.237 Fit side-chains REVERT: A 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8342 (ttp80) REVERT: A 55 GLN cc_start: 0.8828 (tt0) cc_final: 0.8362 (tp-100) REVERT: A 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8482 (mt-10) REVERT: B 20 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8349 (ttp80) REVERT: B 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8373 (tp-100) REVERT: B 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 20 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: C 55 GLN cc_start: 0.8831 (tt0) cc_final: 0.8366 (tp-100) REVERT: C 96 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8486 (mt-10) REVERT: D 20 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: D 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8366 (tp-100) REVERT: D 96 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8475 (mt-10) REVERT: E 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8344 (ttp80) REVERT: E 55 GLN cc_start: 0.8826 (tt0) cc_final: 0.8362 (tp-100) REVERT: E 96 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8470 (mt-10) REVERT: F 20 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8349 (ttp80) REVERT: F 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8363 (tp-100) REVERT: F 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8484 (mt-10) REVERT: G 20 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: G 55 GLN cc_start: 0.8832 (tt0) cc_final: 0.8366 (tp-100) REVERT: G 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8480 (mt-10) REVERT: H 20 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8345 (ttp80) REVERT: H 55 GLN cc_start: 0.8822 (tt0) cc_final: 0.8366 (tp-100) REVERT: H 96 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8477 (mt-10) REVERT: I 20 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: I 55 GLN cc_start: 0.8831 (tt0) cc_final: 0.8366 (tp-100) REVERT: I 96 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8486 (mt-10) REVERT: J 20 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8346 (ttp80) REVERT: J 55 GLN cc_start: 0.8822 (tt0) cc_final: 0.8366 (tp-100) REVERT: J 96 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8477 (mt-10) REVERT: K 20 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8345 (ttp80) REVERT: K 55 GLN cc_start: 0.8822 (tt0) cc_final: 0.8366 (tp-100) REVERT: K 96 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8477 (mt-10) REVERT: L 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8342 (ttp80) REVERT: L 55 GLN cc_start: 0.8828 (tt0) cc_final: 0.8362 (tp-100) REVERT: L 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8482 (mt-10) REVERT: M 20 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: M 55 GLN cc_start: 0.8826 (tt0) cc_final: 0.8363 (tp-100) REVERT: M 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8483 (mt-10) REVERT: N 20 ARG cc_start: 0.8661 (ttp-110) cc_final: 0.8351 (ttp80) REVERT: N 55 GLN cc_start: 0.8832 (tt0) cc_final: 0.8367 (tp-100) REVERT: N 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8480 (mt-10) REVERT: O 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8343 (ttp80) REVERT: O 55 GLN cc_start: 0.8828 (tt0) cc_final: 0.8362 (tp-100) REVERT: O 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8483 (mt-10) REVERT: P 20 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: P 55 GLN cc_start: 0.8831 (tt0) cc_final: 0.8366 (tp-100) REVERT: P 96 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8486 (mt-10) REVERT: Q 20 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8348 (ttp80) REVERT: Q 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8374 (tp-100) REVERT: Q 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8482 (mt-10) REVERT: R 20 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: R 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8366 (tp-100) REVERT: R 96 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8475 (mt-10) REVERT: S 20 ARG cc_start: 0.8653 (ttp-110) cc_final: 0.8344 (ttp80) REVERT: S 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8363 (tp-100) REVERT: S 96 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8469 (mt-10) REVERT: T 20 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8352 (ttp80) REVERT: T 55 GLN cc_start: 0.8831 (tt0) cc_final: 0.8367 (tp-100) REVERT: T 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8480 (mt-10) REVERT: V 20 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8349 (ttp80) REVERT: V 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8363 (tp-100) REVERT: V 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8483 (mt-10) REVERT: W 20 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8344 (ttp80) REVERT: W 55 GLN cc_start: 0.8827 (tt0) cc_final: 0.8363 (tp-100) REVERT: W 96 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8469 (mt-10) REVERT: X 20 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8349 (ttp80) REVERT: X 55 GLN cc_start: 0.8834 (tt0) cc_final: 0.8373 (tp-100) REVERT: X 96 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8482 (mt-10) REVERT: Y 20 ARG cc_start: 0.8657 (ttp-110) cc_final: 0.8347 (ttp80) REVERT: Y 55 GLN cc_start: 0.8819 (tt0) cc_final: 0.8366 (tp-100) REVERT: Y 96 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8476 (mt-10) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.8812 time to fit residues: 511.9198 Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 69 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 chunk 326 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 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 = 0.2954 r_free = 0.2954 target = 0.086707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.077430 restraints weight = 39297.744| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.46 r_work: 0.2653 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9432 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34200 Z= 0.170 Angle : 0.458 4.615 46080 Z= 0.253 Chirality : 0.038 0.132 4752 Planarity : 0.004 0.030 6192 Dihedral : 5.116 44.327 4584 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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: 4.47 (0.13), residues: 4056 helix: 3.83 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.13 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 77 TYR 0.020 0.002 TYR C 37 PHE 0.007 0.001 PHE K 53 TRP 0.006 0.002 TRP C 91 HIS 0.002 0.001 HIS I 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (34200) covalent geometry : angle 0.45797 / 0.25 (46080) hydrogen bonds : bond 0.03880 / 2.61 ( 2616) hydrogen bonds : angle 3.47618 / 2.57 ( 7848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.534 Fit side-chains REVERT: A 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: A 55 GLN cc_start: 0.8805 (tt0) cc_final: 0.8344 (tp-100) REVERT: A 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8492 (mt-10) REVERT: B 20 ARG cc_start: 0.8634 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: B 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8356 (tp-100) REVERT: B 96 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8494 (mt-10) REVERT: C 20 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8316 (ttp80) REVERT: C 55 GLN cc_start: 0.8814 (tt0) cc_final: 0.8348 (tp-100) REVERT: C 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8499 (mt-10) REVERT: D 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: D 55 GLN cc_start: 0.8793 (tt0) cc_final: 0.8345 (tp-100) REVERT: D 96 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8490 (mt-10) REVERT: E 20 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: E 55 GLN cc_start: 0.8806 (tt0) cc_final: 0.8345 (tp-100) REVERT: E 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 20 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8317 (ttp80) REVERT: F 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8340 (tp-100) REVERT: F 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8495 (mt-10) REVERT: G 20 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8317 (ttp80) REVERT: G 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8350 (tp-100) REVERT: G 96 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8483 (mt-10) REVERT: H 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8312 (ttp80) REVERT: H 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8346 (tp-100) REVERT: H 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8495 (mt-10) REVERT: I 20 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8316 (ttp80) REVERT: I 55 GLN cc_start: 0.8814 (tt0) cc_final: 0.8348 (tp-100) REVERT: I 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8499 (mt-10) REVERT: J 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8313 (ttp80) REVERT: J 55 GLN cc_start: 0.8802 (tt0) cc_final: 0.8346 (tp-100) REVERT: J 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8495 (mt-10) REVERT: K 20 ARG cc_start: 0.8622 (ttp-110) cc_final: 0.8313 (ttp80) REVERT: K 55 GLN cc_start: 0.8801 (tt0) cc_final: 0.8346 (tp-100) REVERT: K 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8495 (mt-10) REVERT: L 20 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: L 55 GLN cc_start: 0.8805 (tt0) cc_final: 0.8344 (tp-100) REVERT: L 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8492 (mt-10) REVERT: M 20 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8317 (ttp80) REVERT: M 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8340 (tp-100) REVERT: M 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8495 (mt-10) REVERT: N 20 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8317 (ttp80) REVERT: N 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8351 (tp-100) REVERT: N 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8483 (mt-10) REVERT: O 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8305 (ttp80) REVERT: O 55 GLN cc_start: 0.8805 (tt0) cc_final: 0.8344 (tp-100) REVERT: O 96 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8491 (mt-10) REVERT: P 20 ARG cc_start: 0.8632 (ttp-110) cc_final: 0.8316 (ttp80) REVERT: P 55 GLN cc_start: 0.8814 (tt0) cc_final: 0.8348 (tp-100) REVERT: P 96 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8500 (mt-10) REVERT: Q 20 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: Q 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8356 (tp-100) REVERT: Q 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8494 (mt-10) REVERT: R 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: R 55 GLN cc_start: 0.8793 (tt0) cc_final: 0.8346 (tp-100) REVERT: R 96 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8490 (mt-10) REVERT: S 20 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8311 (ttp80) REVERT: S 55 GLN cc_start: 0.8806 (tt0) cc_final: 0.8345 (tp-100) REVERT: S 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8488 (mt-10) REVERT: T 20 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8317 (ttp80) REVERT: T 55 GLN cc_start: 0.8811 (tt0) cc_final: 0.8351 (tp-100) REVERT: T 96 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8483 (mt-10) REVERT: V 20 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8318 (ttp80) REVERT: V 55 GLN cc_start: 0.8799 (tt0) cc_final: 0.8340 (tp-100) REVERT: V 96 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8495 (mt-10) REVERT: W 20 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8312 (ttp80) REVERT: W 55 GLN cc_start: 0.8806 (tt0) cc_final: 0.8345 (tp-100) REVERT: W 96 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8487 (mt-10) REVERT: X 20 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: X 55 GLN cc_start: 0.8816 (tt0) cc_final: 0.8356 (tp-100) REVERT: X 96 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8494 (mt-10) REVERT: Y 20 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8314 (ttp80) REVERT: Y 55 GLN cc_start: 0.8793 (tt0) cc_final: 0.8346 (tp-100) REVERT: Y 96 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8490 (mt-10) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.9060 time to fit residues: 498.1822 Evaluate side-chains 480 residues out of total 3648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.2937 r_free = 0.2937 target = 0.085721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.076388 restraints weight = 39149.082| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.46 r_work: 0.2635 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9442 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34200 Z= 0.219 Angle : 0.490 4.849 46080 Z= 0.270 Chirality : 0.040 0.134 4752 Planarity : 0.004 0.030 6192 Dihedral : 5.098 43.033 4584 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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: 4.30 (0.13), residues: 4056 helix: 3.70 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 77 TYR 0.022 0.002 TYR X 37 PHE 0.009 0.002 PHE K 53 TRP 0.006 0.002 TRP C 91 HIS 0.003 0.001 HIS V 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (34200) covalent geometry : angle 0.49020 / 0.27 (46080) hydrogen bonds : bond 0.04187 / 2.82 ( 2616) hydrogen bonds : angle 3.53587 / 2.61 ( 7848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13200.74 seconds wall clock time: 225 minutes 57.47 seconds (13557.47 seconds total)