Starting phenix.real_space_refine on Wed Sep 17 03:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zm0_60234/09_2025/8zm0_60234.map" } resolution = 3.1 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= 0.012 sd= 0.134 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: 3 Type Number sf(0) Gaussians C 1984 2.51 5 N 310 2.21 5 O 310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2604 Number of models: 1 Model: "" Number of chains: 1 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Restraints were copied for chains: b, d, f, g, s, B, N, h, n, t, z, C, I, O, i, o, u, 0, D, J, P, j, p, v, 1, k, S, T, V, Y, 6, 7, A, G, M, U, m, 9, y, H, 5, W, 4, X, Z, E, K, Q, c, 8, q, w, 2, F, L, R, e, l, r, x, 3 Time building chain proxies: 0.25, per 1000 atoms: 0.10 Number of scatterers: 2604 At special positions: 0 Unit cell: (57.611, 57.611, 57.611, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 310 8.00 N 310 7.00 C 1984 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: 0.13 Conformation dependent library (CDL) restraints added in 83.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 248 1.29 - 1.35: 186 1.35 - 1.41: 1364 1.41 - 1.47: 310 1.47 - 1.53: 682 Bond restraints: 2790 Sorted by residual: bond pdb=" CB TRP K 210 " pdb=" CG TRP K 210 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 7.98e-01 bond pdb=" CB TRP G 210 " pdb=" CG TRP G 210 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.83e-01 bond pdb=" CB TRP I 210 " pdb=" CG TRP I 210 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.77e-01 bond pdb=" CB TRP u 210 " pdb=" CG TRP u 210 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.68e-01 bond pdb=" CB TRP m 210 " pdb=" CG TRP m 210 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.68e-01 ... (remaining 2785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.41: 2748 0.41 - 0.82: 695 0.82 - 1.23: 151 1.23 - 1.64: 64 1.64 - 2.06: 124 Bond angle restraints: 3782 Sorted by residual: angle pdb=" C TRP q 210 " pdb=" N PHE q 211 " pdb=" CA PHE q 211 " ideal model delta sigma weight residual 121.70 119.64 2.06 1.80e+00 3.09e-01 1.30e+00 angle pdb=" C TRP j 210 " pdb=" N PHE j 211 " pdb=" CA PHE j 211 " ideal model delta sigma weight residual 121.70 119.67 2.03 1.80e+00 3.09e-01 1.27e+00 angle pdb=" C TRP b 210 " pdb=" N PHE b 211 " pdb=" CA PHE b 211 " ideal model delta sigma weight residual 121.70 119.67 2.03 1.80e+00 3.09e-01 1.27e+00 angle pdb=" C TRP i 210 " pdb=" N PHE i 211 " pdb=" CA PHE i 211 " ideal model delta sigma weight residual 121.70 119.68 2.02 1.80e+00 3.09e-01 1.26e+00 angle pdb=" C TRP r 210 " pdb=" N PHE r 211 " pdb=" CA PHE r 211 " ideal model delta sigma weight residual 121.70 119.69 2.01 1.80e+00 3.09e-01 1.24e+00 ... (remaining 3777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.92: 818 6.92 - 13.83: 176 13.83 - 20.75: 60 20.75 - 27.67: 0 27.67 - 34.58: 62 Dihedral angle restraints: 1116 sinusoidal: 372 harmonic: 744 Sorted by residual: dihedral pdb=" CA TYR y 208 " pdb=" CB TYR y 208 " pdb=" CG TYR y 208 " pdb=" CD1 TYR y 208 " ideal model delta sinusoidal sigma weight residual -20.00 -54.58 34.58 2 2.00e+01 2.50e-03 3.87e+00 dihedral pdb=" CA TYR 2 208 " pdb=" CB TYR 2 208 " pdb=" CG TYR 2 208 " pdb=" CD1 TYR 2 208 " ideal model delta sinusoidal sigma weight residual -20.00 -54.54 34.54 2 2.00e+01 2.50e-03 3.86e+00 dihedral pdb=" CA TYR 7 208 " pdb=" CB TYR 7 208 " pdb=" CG TYR 7 208 " pdb=" CD1 TYR 7 208 " ideal model delta sinusoidal sigma weight residual -20.00 -54.53 34.53 2 2.00e+01 2.50e-03 3.86e+00 ... (remaining 1113 not shown) Histogram of chiral volume deviations from ideal: 0.011 - 0.028: 68 0.028 - 0.045: 97 0.045 - 0.062: 21 0.062 - 0.080: 0 0.080 - 0.097: 62 Chirality restraints: 248 Sorted by residual: chirality pdb=" CA PHE 1 211 " pdb=" N PHE 1 211 " pdb=" C PHE 1 211 " pdb=" CB PHE 1 211 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.34e-01 chirality pdb=" CA PHE E 211 " pdb=" N PHE E 211 " pdb=" C PHE E 211 " pdb=" CB PHE E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.32e-01 chirality pdb=" CA PHE T 211 " pdb=" N PHE T 211 " pdb=" C PHE T 211 " pdb=" CB PHE T 211 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.31e-01 ... (remaining 245 not shown) Planarity restraints: 372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 211 " -0.006 2.00e-02 2.50e+03 4.87e-03 4.15e-01 pdb=" CG PHE 5 211 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 211 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 211 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 211 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 211 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 5 211 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 211 " -0.006 2.00e-02 2.50e+03 4.86e-03 4.14e-01 pdb=" CG PHE P 211 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE P 211 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE P 211 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE P 211 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE P 211 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE P 211 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 211 " -0.006 2.00e-02 2.50e+03 4.83e-03 4.08e-01 pdb=" CG PHE Q 211 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 211 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 211 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 211 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 211 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE Q 211 " -0.002 2.00e-02 2.50e+03 ... (remaining 369 not shown) Histogram of nonbonded interaction distances: 2.71 - 3.15: 1696 3.15 - 3.59: 2545 3.59 - 4.02: 4614 4.02 - 4.46: 5209 4.46 - 4.90: 8314 Nonbonded interactions: 22378 Sorted by model distance: nonbonded pdb=" O TRP P 210 " pdb=" CA PHE P 211 " model vdw 2.710 2.776 nonbonded pdb=" O TRP c 210 " pdb=" CA PHE c 211 " model vdw 2.710 2.776 nonbonded pdb=" O TRP x 210 " pdb=" CA PHE x 211 " model vdw 2.710 2.776 nonbonded pdb=" O TRP j 210 " pdb=" CA PHE j 211 " model vdw 2.710 2.776 nonbonded pdb=" O TRP 5 210 " pdb=" CA PHE 5 211 " model vdw 2.710 2.776 ... (remaining 22373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 's' selection = chain 'B' selection = chain 'N' selection = chain 'h' selection = chain 'n' selection = chain 't' selection = chain 'z' selection = chain 'C' selection = chain 'I' selection = chain 'O' selection = chain 'i' selection = chain 'o' selection = chain 'u' selection = chain '0' selection = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'j' selection = chain 'p' selection = chain 'v' selection = chain '1' selection = chain 'k' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'G' selection = chain 'M' selection = chain 'U' selection = chain 'm' selection = chain '9' selection = chain 'y' selection = chain 'H' selection = chain '5' selection = chain 'W' selection = chain '4' selection = chain 'X' selection = chain 'Z' selection = chain 'E' selection = chain 'K' selection = chain 'Q' selection = chain 'c' selection = chain '8' selection = chain 'q' selection = chain 'w' selection = chain '2' selection = chain 'F' selection = chain 'L' selection = chain 'R' selection = chain 'e' selection = chain 'l' selection = chain 'r' selection = chain 'x' selection = chain '3' } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.009 0.028 2790 Z= 0.412 Angle : 0.530 2.056 3782 Z= 0.273 Chirality : 0.054 0.097 248 Planarity : 0.003 0.005 372 Dihedral : 12.835 34.583 620 Min Nonbonded Distance : 2.710 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -8.10 (0.11), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.17 (0.08), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR f 208 PHE 0.011 0.003 PHE P 211 TRP 0.009 0.003 TRP e 210 Details of bonding type rmsd covalent geometry : bond 0.00923 ( 2790) covalent geometry : angle 0.53001 ( 3782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.053 Fit side-chains REVERT: m 208 TYR cc_start: 0.8728 (m-80) cc_final: 0.8464 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0383 time to fit residues: 2.8876 Evaluate side-chains 35 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.081447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.067651 restraints weight = 5772.945| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 3.36 r_work: 0.2562 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.164 2790 Z= 3.291 Angle : 2.783 12.565 3782 Z= 1.565 Chirality : 0.284 0.600 248 Planarity : 0.018 0.036 372 Dihedral : 8.978 19.057 248 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 aren not related in a simple way. whole: -7.70 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.86 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.055 0.009 TYR k 208 PHE 0.081 0.018 PHE j 211 TRP 0.070 0.023 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07168 ( 2790) covalent geometry : angle 2.78329 ( 3782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.060 Fit side-chains REVERT: o 208 TYR cc_start: 0.9238 (m-10) cc_final: 0.8746 (m-10) REVERT: K 208 TYR cc_start: 0.9257 (m-10) cc_final: 0.8770 (m-10) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0383 time to fit residues: 0.9233 Evaluate side-chains 16 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.080378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.066886 restraints weight = 5848.798| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.36 r_work: 0.2556 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.170 2790 Z= 3.291 Angle : 2.917 13.477 3782 Z= 1.642 Chirality : 0.282 0.596 248 Planarity : 0.018 0.035 372 Dihedral : 9.109 20.481 248 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 4.30 % Allowed : 9.14 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.86 (0.14), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.98 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.034 0.009 TYR s 208 PHE 0.079 0.018 PHE j 211 TRP 0.071 0.023 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07187 ( 2790) covalent geometry : angle 2.91667 ( 3782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.078 Fit side-chains REVERT: o 208 TYR cc_start: 0.9251 (m-80) cc_final: 0.8852 (m-10) REVERT: 0 211 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7902 (p90) REVERT: T 208 TYR cc_start: 0.9299 (m-80) cc_final: 0.8872 (m-10) REVERT: V 211 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7986 (p90) REVERT: K 208 TYR cc_start: 0.9259 (m-10) cc_final: 0.8855 (m-10) REVERT: c 211 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7780 (p90) REVERT: x 211 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8041 (p90) outliers start: 8 outliers final: 2 residues processed: 28 average time/residue: 0.0374 time to fit residues: 1.4328 Evaluate side-chains 25 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.080534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.067081 restraints weight = 5799.398| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 3.33 r_work: 0.2548 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.171 2790 Z= 3.290 Angle : 2.898 14.196 3782 Z= 1.634 Chirality : 0.279 0.593 248 Planarity : 0.018 0.036 372 Dihedral : 9.242 20.692 248 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 3.23 % Allowed : 12.37 % Favored : 84.41 % 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 aren not related in a simple way. whole: -7.82 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.95 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.009 TYR s 208 PHE 0.080 0.018 PHE A 211 TRP 0.072 0.023 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07187 ( 2790) covalent geometry : angle 2.89805 ( 3782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.064 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7896 (p90) REVERT: V 211 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7997 (p90) REVERT: K 208 TYR cc_start: 0.9245 (m-80) cc_final: 0.8841 (m-10) REVERT: c 211 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7859 (p90) REVERT: x 211 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7972 (p90) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.0268 time to fit residues: 0.9383 Evaluate side-chains 23 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.080547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.067096 restraints weight = 5796.259| |-----------------------------------------------------------------------------| r_work (start): 0.2627 rms_B_bonded: 3.33 r_work: 0.2556 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.288 Angle : 2.923 13.176 3782 Z= 1.647 Chirality : 0.280 0.595 248 Planarity : 0.018 0.035 372 Dihedral : 9.227 20.582 248 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 26.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 5.91 % Allowed : 10.75 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.83 (0.14), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.030 0.009 TYR s 208 PHE 0.078 0.017 PHE A 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07184 ( 2790) covalent geometry : angle 2.92346 ( 3782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.055 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7899 (p90) REVERT: V 211 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8003 (p90) REVERT: c 211 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7865 (p90) REVERT: w 211 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8214 (p90) REVERT: x 211 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7933 (p90) outliers start: 11 outliers final: 4 residues processed: 31 average time/residue: 0.0269 time to fit residues: 1.1480 Evaluate side-chains 27 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.067142 restraints weight = 5796.912| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.32 r_work: 0.2551 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.289 Angle : 2.914 14.168 3782 Z= 1.644 Chirality : 0.279 0.589 248 Planarity : 0.018 0.035 372 Dihedral : 9.208 20.936 248 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 6.99 % Allowed : 9.68 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.83 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.038 0.009 TYR J 208 PHE 0.077 0.017 PHE j 211 TRP 0.073 0.023 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07183 ( 2790) covalent geometry : angle 2.91368 ( 3782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.055 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7884 (p90) REVERT: j 211 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8667 (p90) REVERT: V 211 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8001 (p90) REVERT: A 211 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8651 (p90) REVERT: K 208 TYR cc_start: 0.9210 (m-10) cc_final: 0.8654 (m-10) REVERT: c 211 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7862 (p90) REVERT: w 211 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8207 (p90) REVERT: x 211 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.7845 (p90) outliers start: 13 outliers final: 5 residues processed: 32 average time/residue: 0.0290 time to fit residues: 1.2657 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain n residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain j residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.080592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.067084 restraints weight = 5842.087| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.34 r_work: 0.2552 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.287 Angle : 2.923 13.511 3782 Z= 1.648 Chirality : 0.280 0.592 248 Planarity : 0.018 0.035 372 Dihedral : 9.206 20.906 248 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 8.60 % Allowed : 8.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.84 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.009 TYR s 208 PHE 0.077 0.017 PHE j 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07180 ( 2790) covalent geometry : angle 2.92348 ( 3782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 16 time to evaluate : 0.087 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7886 (p90) REVERT: j 211 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8663 (p90) REVERT: V 211 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7888 (p90) REVERT: A 211 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8649 (p90) REVERT: 5 211 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8313 (p90) REVERT: K 208 TYR cc_start: 0.9223 (m-80) cc_final: 0.8751 (m-10) REVERT: c 211 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7859 (p90) REVERT: w 211 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8215 (p90) REVERT: x 211 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7927 (p90) outliers start: 16 outliers final: 6 residues processed: 32 average time/residue: 0.0246 time to fit residues: 1.1098 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain n residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain j residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain 5 residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.080597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.067071 restraints weight = 5903.716| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.37 r_work: 0.2551 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.289 Angle : 2.918 14.395 3782 Z= 1.646 Chirality : 0.279 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.191 20.910 248 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 7.53 % Allowed : 9.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.84 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.009 TYR s 208 PHE 0.077 0.017 PHE j 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07187 ( 2790) covalent geometry : angle 2.91764 ( 3782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.073 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7884 (p90) REVERT: j 211 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8638 (p90) REVERT: V 211 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7998 (p90) REVERT: A 211 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8626 (p90) REVERT: K 208 TYR cc_start: 0.9174 (m-80) cc_final: 0.8695 (m-10) REVERT: c 211 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7849 (p90) REVERT: w 211 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8195 (p90) REVERT: x 211 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7904 (p90) outliers start: 14 outliers final: 6 residues processed: 30 average time/residue: 0.0364 time to fit residues: 1.5340 Evaluate side-chains 29 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 16 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain n residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain j residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.080598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.067116 restraints weight = 5898.357| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.35 r_work: 0.2553 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.288 Angle : 2.922 13.212 3782 Z= 1.647 Chirality : 0.280 0.593 248 Planarity : 0.018 0.035 372 Dihedral : 9.187 20.803 248 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 7.53 % Allowed : 9.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.84 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.027 0.009 TYR p 208 PHE 0.077 0.017 PHE j 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07183 ( 2790) covalent geometry : angle 2.92159 ( 3782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 17 time to evaluate : 0.085 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7881 (p90) REVERT: j 211 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8634 (p90) REVERT: V 211 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7878 (p90) REVERT: A 211 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8625 (p90) REVERT: 5 211 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8278 (p90) REVERT: K 208 TYR cc_start: 0.9165 (m-80) cc_final: 0.8701 (m-10) REVERT: c 211 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7849 (p90) REVERT: w 211 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8196 (p90) REVERT: x 211 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7906 (p90) outliers start: 14 outliers final: 6 residues processed: 31 average time/residue: 0.0342 time to fit residues: 1.4697 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain n residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain j residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain 5 residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.067146 restraints weight = 5869.562| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.34 r_work: 0.2547 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.291 Angle : 2.919 13.143 3782 Z= 1.646 Chirality : 0.280 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.192 20.859 248 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 7.53 % Allowed : 9.68 % Favored : 82.80 % 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 aren not related in a simple way. whole: -7.84 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.009 TYR J 208 PHE 0.078 0.017 PHE j 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07189 ( 2790) covalent geometry : angle 2.91856 ( 3782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 248 Ramachandran restraints generated. 124 Oldfield, 0 Emsley, 124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.073 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7885 (p90) REVERT: j 211 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8635 (p90) REVERT: V 211 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7885 (p90) REVERT: A 211 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.8625 (p90) REVERT: 5 211 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8280 (p90) REVERT: K 208 TYR cc_start: 0.9168 (m-80) cc_final: 0.8705 (m-10) REVERT: c 211 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7851 (p90) REVERT: w 211 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8195 (p90) REVERT: x 211 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7905 (p90) outliers start: 14 outliers final: 6 residues processed: 30 average time/residue: 0.0349 time to fit residues: 1.4514 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 16 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 211 PHE Chi-restraints excluded: chain n residue 211 PHE Chi-restraints excluded: chain 0 residue 211 PHE Chi-restraints excluded: chain P residue 211 PHE Chi-restraints excluded: chain j residue 211 PHE Chi-restraints excluded: chain V residue 211 PHE Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain 5 residue 211 PHE Chi-restraints excluded: chain W residue 211 PHE Chi-restraints excluded: chain c residue 211 PHE Chi-restraints excluded: chain w residue 211 PHE Chi-restraints excluded: chain 2 residue 211 PHE Chi-restraints excluded: chain L residue 211 PHE Chi-restraints excluded: chain x residue 211 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.080645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.067095 restraints weight = 5879.232| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 3.36 r_work: 0.2549 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 0.172 2790 Z= 3.291 Angle : 2.920 13.172 3782 Z= 1.646 Chirality : 0.279 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.197 20.873 248 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 29.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 7.53 % Allowed : 9.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.84 (0.15), residues: 124 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.11), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.009 TYR L 208 PHE 0.078 0.017 PHE A 211 TRP 0.073 0.024 TRP 6 210 Details of bonding type rmsd covalent geometry : bond 0.07190 ( 2790) covalent geometry : angle 2.91960 ( 3782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 428.35 seconds wall clock time: 8 minutes 0.70 seconds (480.70 seconds total)