Starting phenix.real_space_refine on Wed Jun 4 11:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zm0_60234/06_2025/8zm0_60234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zm0_60234/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zm0_60234/06_2025/8zm0_60234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zm0_60234/06_2025/8zm0_60234.map" model { file = "/net/cci-nas-00/data/ceres_data/8zm0_60234/06_2025/8zm0_60234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zm0_60234/06_2025/8zm0_60234.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2604 Number of models: 1 Model: "" Number of chains: 1 Chain: "1" 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: 0, 3, 2, 5, 4, 7, 6, 9, 8, A, C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n, q, p, s, r, u, t, w, v, y, x, z Time building chain proxies: 0.63, per 1000 atoms: 0.24 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: 0.71 Conformation dependent library (CDL) restraints added in 141.3 milliseconds 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: 0.47 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: 0.84 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: 0.03 Found NCS groups: ncs_group { reference = chain '1' selection = chain '0' selection = chain '3' selection = chain '2' selection = chain '5' selection = chain '4' selection = chain '7' selection = chain '6' selection = chain '9' selection = chain '8' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' selection = chain 'q' selection = chain 'p' selection = chain 's' selection = chain 'r' selection = chain 'u' selection = chain 't' selection = chain 'w' selection = chain 'v' selection = chain 'y' selection = chain 'x' selection = chain 'z' } 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: 0.350 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.540 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.003 TRP e 210 PHE 0.011 0.003 PHE P 211 TYR 0.008 0.002 TYR f 208 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 : 0.265 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: 0.1068 time to fit residues: 7.9227 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 : 0.262 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.067713 restraints weight = 5680.796| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.33 r_work: 0.2563 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.070 0.023 TRP 6 210 PHE 0.081 0.018 PHE j 211 TYR 0.055 0.009 TYR k 208 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 : 0.263 Fit side-chains REVERT: o 208 TYR cc_start: 0.9231 (m-10) cc_final: 0.8739 (m-10) REVERT: K 208 TYR cc_start: 0.9252 (m-10) cc_final: 0.8764 (m-10) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0997 time to fit residues: 2.4530 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 : 0.289 ------------------------------------------------------------------------------- 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 = 0.2662 r_free = 0.2662 target = 0.066964 restraints weight = 5721.276| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.33 r_work: 0.2567 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.071 0.023 TRP 6 210 PHE 0.079 0.018 PHE j 211 TYR 0.034 0.009 TYR s 208 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 : 0.287 Fit side-chains REVERT: o 208 TYR cc_start: 0.9256 (m-80) cc_final: 0.8858 (m-10) REVERT: 0 211 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7908 (p90) REVERT: T 208 TYR cc_start: 0.9305 (m-80) cc_final: 0.8881 (m-10) REVERT: V 211 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.7991 (p90) REVERT: K 208 TYR cc_start: 0.9263 (m-10) cc_final: 0.8862 (m-10) REVERT: c 211 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7785 (p90) REVERT: x 211 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8043 (p90) outliers start: 8 outliers final: 2 residues processed: 28 average time/residue: 0.1035 time to fit residues: 3.9255 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 : 0.278 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.067037 restraints weight = 5855.067| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 3.35 r_work: 0.2549 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.072 0.023 TRP 6 210 PHE 0.080 0.018 PHE A 211 TYR 0.036 0.009 TYR s 208 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 : 0.257 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7899 (p90) REVERT: V 211 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7999 (p90) REVERT: K 208 TYR cc_start: 0.9247 (m-80) cc_final: 0.8843 (m-10) REVERT: c 211 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7860 (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: 0.0938 time to fit residues: 3.0865 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 : 0.243 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.067133 restraints weight = 5743.863| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.31 r_work: 0.2554 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.024 TRP 6 210 PHE 0.078 0.017 PHE A 211 TYR 0.030 0.009 TYR s 208 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 : 0.244 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7900 (p90) REVERT: V 211 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8005 (p90) REVERT: c 211 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7863 (p90) REVERT: w 211 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8212 (p90) REVERT: x 211 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.7929 (p90) outliers start: 11 outliers final: 4 residues processed: 31 average time/residue: 0.0932 time to fit residues: 3.8747 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 : 0.283 ------------------------------------------------------------------------------- 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 = 0.2663 r_free = 0.2663 target = 0.067095 restraints weight = 5868.951| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.35 r_work: 0.2549 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.023 TRP 6 210 PHE 0.077 0.017 PHE j 211 TYR 0.038 0.009 TYR J 208 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 : 0.296 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7852 (p90) REVERT: j 211 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8636 (p90) REVERT: V 211 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7993 (p90) REVERT: A 211 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8627 (p90) REVERT: K 208 TYR cc_start: 0.9154 (m-10) cc_final: 0.8583 (m-10) REVERT: c 211 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7853 (p90) REVERT: w 211 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8191 (p90) REVERT: x 211 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7822 (p90) outliers start: 13 outliers final: 5 residues processed: 32 average time/residue: 0.1015 time to fit residues: 4.3838 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 : 0.298 ------------------------------------------------------------------------------- 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 = 0.080603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.067099 restraints weight = 5866.803| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.35 r_work: 0.2553 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 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 : 2.924 13.511 3782 Z= 1.648 Chirality : 0.280 0.592 248 Planarity : 0.018 0.035 372 Dihedral : 9.205 20.902 248 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.024 TRP 6 210 PHE 0.077 0.017 PHE j 211 TYR 0.028 0.009 TYR s 208 Details of bonding type rmsd covalent geometry : bond 0.07180 ( 2790) covalent geometry : angle 2.92350 ( 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 : 0.272 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7852 (p90) REVERT: j 211 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8636 (p90) REVERT: V 211 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 211 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (p90) REVERT: 5 211 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8277 (p90) REVERT: K 208 TYR cc_start: 0.9165 (m-80) cc_final: 0.8684 (m-10) REVERT: c 211 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7849 (p90) REVERT: w 211 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8194 (p90) REVERT: x 211 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7902 (p90) outliers start: 16 outliers final: 6 residues processed: 32 average time/residue: 0.0962 time to fit residues: 4.1272 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 : 0.275 ------------------------------------------------------------------------------- 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 = 0.080618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.067143 restraints weight = 5838.511| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.34 r_work: 0.2552 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 2.917 14.345 3782 Z= 1.645 Chirality : 0.279 0.591 248 Planarity : 0.018 0.035 372 Dihedral : 9.197 20.871 248 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 27.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 43.55 % Favored : 56.45 % Rotamer: Outliers : 8.06 % Allowed : 8.60 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.024 TRP 6 210 PHE 0.077 0.017 PHE j 211 TYR 0.028 0.009 TYR s 208 Details of bonding type rmsd covalent geometry : bond 0.07187 ( 2790) covalent geometry : angle 2.91715 ( 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 31 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 16 time to evaluate : 0.310 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7914 (p90) REVERT: j 211 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8666 (p90) REVERT: V 211 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.7882 (p90) REVERT: A 211 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8646 (p90) REVERT: 5 211 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8310 (p90) REVERT: K 208 TYR cc_start: 0.9226 (m-80) cc_final: 0.8756 (m-10) REVERT: c 211 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7857 (p90) REVERT: w 211 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8212 (p90) REVERT: x 211 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.7926 (p90) outliers start: 15 outliers final: 6 residues processed: 31 average time/residue: 0.0975 time to fit residues: 4.0986 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 : 0.253 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.080605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.067139 restraints weight = 5893.159| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.35 r_work: 0.2550 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4230 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 : 2.922 13.204 3782 Z= 1.647 Chirality : 0.280 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.198 20.850 248 Min Nonbonded Distance : 2.357 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.074 0.024 TRP 6 210 PHE 0.078 0.017 PHE j 211 TYR 0.026 0.009 TYR p 208 Details of bonding type rmsd covalent geometry : bond 0.07180 ( 2790) covalent geometry : angle 2.92208 ( 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 : 0.275 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7881 (p90) REVERT: j 211 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (p90) REVERT: V 211 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7880 (p90) REVERT: A 211 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8626 (p90) REVERT: 5 211 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8279 (p90) REVERT: K 208 TYR cc_start: 0.9166 (m-80) cc_final: 0.8703 (m-10) REVERT: c 211 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7848 (p90) REVERT: w 211 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8196 (p90) REVERT: x 211 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7909 (p90) outliers start: 14 outliers final: 6 residues processed: 31 average time/residue: 0.1003 time to fit residues: 4.2056 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 : 0.282 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.080664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.067217 restraints weight = 5737.943| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 3.31 r_work: 0.2557 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4239 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 13.157 3782 Z= 1.646 Chirality : 0.280 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.196 20.860 248 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 30.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.024 TRP 6 210 PHE 0.078 0.017 PHE A 211 TYR 0.029 0.009 TYR J 208 Details of bonding type rmsd covalent geometry : bond 0.07190 ( 2790) covalent geometry : angle 2.91852 ( 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 : 0.282 Fit side-chains REVERT: 0 211 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.7913 (p90) REVERT: j 211 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8666 (p90) REVERT: V 211 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 211 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8644 (p90) REVERT: 5 211 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8314 (p90) REVERT: K 208 TYR cc_start: 0.9224 (m-80) cc_final: 0.8768 (m-10) REVERT: c 211 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7859 (p90) REVERT: w 211 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8208 (p90) REVERT: x 211 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.7929 (p90) outliers start: 14 outliers final: 6 residues processed: 30 average time/residue: 0.0968 time to fit residues: 3.9422 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 : 0.280 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.080677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.067223 restraints weight = 5823.299| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.33 r_work: 0.2553 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2467 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4239 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 13.214 3782 Z= 1.646 Chirality : 0.279 0.590 248 Planarity : 0.018 0.035 372 Dihedral : 9.198 20.861 248 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 : 9.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.073 0.023 TRP 6 210 PHE 0.078 0.017 PHE j 211 TYR 0.030 0.009 TYR L 208 Details of bonding type rmsd covalent geometry : bond 0.07190 ( 2790) covalent geometry : angle 2.91928 ( 3782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 943.82 seconds wall clock time: 16 minutes 59.78 seconds (1019.78 seconds total)