Starting phenix.real_space_refine on Thu Oct 22 19:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mga_48244/10_2026/9mga_48244.map" } resolution = 2.85 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= 0.002 sd= 0.033 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 3423 2.51 5 N 525 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4599 Number of models: 1 Model: "" Number of chains: 3 Chain: "0" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 0 1 " pdbres="PHE 0 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 67 Unusual residues: {'I7L': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4, None: 1} Not linked: pdbres="I7L 1 1 " pdbres="PHE 1 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'I7L': 1} Classifications: {'peptide': 7, 'undetermined': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5, None: 1} Not linked: pdbres="I7L 2 1 " pdbres="PHE 2 2 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'I7L:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: 3, 6, 9, AA, C, F, I, L, O, R, U, X, c, f, i, l, o, r, u, x, 4, 7, A, D, G, J, M, P, S, V, Y, a, d, g, j, m, p, s, v, y, 5, 8, B, E, H, K, N, Q, T, W, Z, b, e, h, k, n, q, t, w, z Time building chain proxies: 0.74, per 1000 atoms: 0.16 Number of scatterers: 4599 At special positions: 0 Unit cell: (81.03, 82.14, 57.72, 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 651 8.00 N 525 7.00 C 3423 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=63, symmetry=0 Number of additional bonds: simple=63, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 90.5 milliseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 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: 0.46 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: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.27: 588 1.27 - 1.38: 2216 1.38 - 1.49: 892 1.49 - 1.60: 1092 1.60 - 1.71: 63 Bond restraints: 4851 Sorted by residual: bond pdb=" C02 I7L c 1 " pdb=" C04 I7L c 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L S 1 " pdb=" C04 I7L S 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L x 1 " pdb=" C04 I7L x 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C02 I7L G 1 " pdb=" C04 I7L G 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C02 I7L R 1 " pdb=" C04 I7L R 1 " ideal model delta sigma weight residual 1.555 1.714 -0.159 2.00e-02 2.50e+03 6.29e+01 ... (remaining 4846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.16: 6132 5.16 - 10.32: 189 10.32 - 15.48: 21 15.48 - 20.63: 21 20.63 - 25.79: 63 Bond angle restraints: 6426 Sorted by residual: angle pdb=" C04 I7L n 1 " pdb=" C02 I7L n 1 " pdb=" O01 I7L n 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L T 1 " pdb=" C02 I7L T 1 " pdb=" O01 I7L T 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L 5 1 " pdb=" C02 I7L 5 1 " pdb=" O01 I7L 5 1 " ideal model delta sigma weight residual 115.75 89.96 25.79 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C04 I7L h 1 " pdb=" C02 I7L h 1 " pdb=" O01 I7L h 1 " ideal model delta sigma weight residual 115.75 89.97 25.78 3.00e+00 1.11e-01 7.38e+01 angle pdb=" C04 I7L Q 1 " pdb=" C02 I7L Q 1 " pdb=" O01 I7L Q 1 " ideal model delta sigma weight residual 115.75 89.98 25.77 3.00e+00 1.11e-01 7.38e+01 ... (remaining 6421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 1764 14.13 - 28.27: 273 28.27 - 42.40: 63 42.40 - 56.53: 84 56.53 - 70.67: 21 Dihedral angle restraints: 2205 sinusoidal: 1071 harmonic: 1134 Sorted by residual: dihedral pdb=" N PHE O 2 " pdb=" C PHE O 2 " pdb=" CA PHE O 2 " pdb=" CB PHE O 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE L 2 " pdb=" C PHE L 2 " pdb=" CA PHE L 2 " pdb=" CB PHE L 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N PHE f 2 " pdb=" C PHE f 2 " pdb=" CA PHE f 2 " pdb=" CB PHE f 2 " ideal model delta harmonic sigma weight residual 122.80 112.94 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 2202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 252 0.054 - 0.107: 42 0.107 - 0.161: 0 0.161 - 0.215: 42 0.215 - 0.268: 21 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA PHE I 2 " pdb=" N PHE I 2 " pdb=" C PHE I 2 " pdb=" CB PHE I 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE R 2 " pdb=" N PHE R 2 " pdb=" C PHE R 2 " pdb=" CB PHE R 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PHE F 2 " pdb=" N PHE F 2 " pdb=" C PHE F 2 " pdb=" CB PHE F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 354 not shown) Planarity restraints: 777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE y 3 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.15e+00 pdb=" CG PHE y 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE y 3 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE y 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE y 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE y 3 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE y 3 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE p 3 " -0.020 2.00e-02 2.50e+03 2.16e-02 8.13e+00 pdb=" CG PHE p 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE p 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE p 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE p 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE p 3 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE p 3 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 3 " -0.020 2.00e-02 2.50e+03 2.15e-02 8.12e+00 pdb=" CG PHE P 3 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE P 3 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE P 3 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE P 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 3 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE P 3 " -0.013 2.00e-02 2.50e+03 ... (remaining 774 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 2592 3.02 - 3.49: 2724 3.49 - 3.96: 5947 3.96 - 4.43: 8231 4.43 - 4.90: 13054 Nonbonded interactions: 32548 Sorted by model distance: nonbonded pdb=" O PHE P 2 " pdb=" O PHE Y 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 4 2 " pdb=" O PHE d 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 1 2 " pdb=" O PHE a 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE 7 2 " pdb=" O PHE g 3 " model vdw 2.556 3.040 nonbonded pdb=" O PHE A 2 " pdb=" O PHE M 3 " model vdw 2.556 3.040 ... (remaining 32543 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: 0.01 Found NCS groups: ncs_group { reference = (chain '0' and resid 1 through 7) selection = chain '1' selection = (chain '2' and resid 1 through 7) selection = (chain '3' and resid 1 through 7) selection = chain '4' selection = (chain '5' and resid 1 through 7) selection = (chain '6' and resid 1 through 7) selection = chain '7' selection = (chain '8' and resid 1 through 7) selection = (chain '9' and resid 1 through 7) selection = chain 'A' selection = (chain 'AA' and resid 1 through 7) selection = (chain 'B' and resid 1 through 7) selection = (chain 'C' and resid 1 through 7) selection = chain 'D' selection = (chain 'E' and resid 1 through 7) selection = (chain 'F' and resid 1 through 7) selection = chain 'G' selection = (chain 'H' and resid 1 through 7) selection = (chain 'I' and resid 1 through 7) selection = chain 'J' selection = (chain 'K' and resid 1 through 7) selection = (chain 'L' and resid 1 through 7) selection = chain 'M' selection = (chain 'N' and resid 1 through 7) selection = (chain 'O' and resid 1 through 7) selection = chain 'P' selection = (chain 'Q' and resid 1 through 7) selection = (chain 'R' and resid 1 through 7) selection = chain 'S' selection = (chain 'T' and resid 1 through 7) selection = (chain 'U' and resid 1 through 7) selection = chain 'V' selection = (chain 'W' and resid 1 through 7) selection = (chain 'X' and resid 1 through 7) selection = chain 'Y' selection = (chain 'Z' and resid 1 through 7) selection = chain 'a' selection = (chain 'b' and resid 1 through 7) selection = (chain 'c' and resid 1 through 7) selection = chain 'd' selection = (chain 'e' and resid 1 through 7) selection = (chain 'f' and resid 1 through 7) selection = chain 'g' selection = (chain 'h' and resid 1 through 7) selection = (chain 'i' and resid 1 through 7) selection = chain 'j' selection = (chain 'k' and resid 1 through 7) selection = (chain 'l' and resid 1 through 7) selection = chain 'm' selection = (chain 'n' and resid 1 through 7) selection = (chain 'o' and resid 1 through 7) selection = chain 'p' selection = (chain 'q' and resid 1 through 7) selection = (chain 'r' and resid 1 through 7) selection = chain 's' selection = (chain 't' and resid 1 through 7) selection = (chain 'u' and resid 1 through 7) selection = chain 'v' selection = (chain 'w' and resid 1 through 7) selection = (chain 'x' and resid 1 through 7) selection = chain 'y' selection = (chain 'z' and resid 1 through 7) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.670 Find NCS groups from input model: 0.110 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.035 0.159 4914 Z= 1.867 Angle : 3.300 25.793 6426 Z= 1.434 Chirality : 0.094 0.268 357 Planarity : 0.016 0.062 777 Dihedral : 18.894 70.665 1491 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.88 % Allowed : 11.76 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.19), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.15), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR 1 7 PHE 0.047 0.011 PHE y 3 Details of bonding type rmsd/Z covalent geometry : bond 0.03489 / 1.86 ( 4851) covalent geometry : angle 3.29981 / 1.43 ( 6426) Misc. bond : bond 0.02035 / 1.18 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 32 time to evaluate : 0.171 Fit side-chains REVERT: D 7 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5131 (m-80) REVERT: M 7 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: V 7 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: 4 7 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7183 (m-80) REVERT: 7 7 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: j 7 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.6029 (m-80) outliers start: 21 outliers final: 3 residues processed: 53 average time/residue: 0.3595 time to fit residues: 20.2088 Evaluate side-chains 36 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain J residue 7 TYR Chi-restraints excluded: chain M residue 7 TYR Chi-restraints excluded: chain V residue 7 TYR Chi-restraints excluded: chain 1 residue 7 TYR Chi-restraints excluded: chain 4 residue 7 TYR Chi-restraints excluded: chain 7 residue 7 TYR Chi-restraints excluded: chain j residue 7 TYR Chi-restraints excluded: chain s residue 7 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN N 8 GLN Z 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.065786 restraints weight = 8554.049| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.43 r_work: 0.2800 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4914 Z= 0.128 Angle : 0.453 2.840 6426 Z= 0.236 Chirality : 0.026 0.054 357 Planarity : 0.012 0.066 777 Dihedral : 10.120 34.637 627 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.28 % Allowed : 12.61 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.21), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.16), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR r 7 PHE 0.008 0.001 PHE 5 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.13 ( 4851) covalent geometry : angle 0.45330 / 0.24 ( 6426) Misc. bond : bond 0.00036 / 0.02 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.122 Fit side-chains REVERT: E 8 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: V 6 GLN cc_start: 0.8319 (pt0) cc_final: 0.8091 (pt0) REVERT: w 8 GLN cc_start: 0.7914 (mm110) cc_final: 0.5440 (pt0) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.7607 time to fit residues: 37.5529 Evaluate side-chains 41 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN T 8 GLN 5 8 GLN 8 8 GLN e 8 GLN q 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.067412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.056050 restraints weight = 8771.276| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.29 r_work: 0.2652 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.052 4914 Z= 0.506 Angle : 0.741 4.882 6426 Z= 0.405 Chirality : 0.047 0.122 357 Planarity : 0.014 0.079 777 Dihedral : 18.117 59.621 609 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.40 % Allowed : 15.13 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.19), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.15), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR I 7 PHE 0.028 0.003 PHE M 3 Details of bonding type rmsd/Z covalent geometry : bond 0.01265 / 0.51 ( 4851) covalent geometry : angle 0.74054 / 0.40 ( 6426) Misc. bond : bond 0.00150 / 0.08 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.123 Fit side-chains REVERT: E 8 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: H 8 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: M 6 GLN cc_start: 0.8687 (pt0) cc_final: 0.8385 (pt0) REVERT: V 6 GLN cc_start: 0.8461 (pt0) cc_final: 0.8202 (pt0) REVERT: n 8 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7696 (mm-40) REVERT: t 8 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8202 (mm-40) outliers start: 5 outliers final: 0 residues processed: 55 average time/residue: 0.8916 time to fit residues: 50.2453 Evaluate side-chains 52 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN N 8 GLN T 8 GLN W 8 GLN 5 8 GLN k 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.069802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.057844 restraints weight = 8699.411| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.45 r_work: 0.2696 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4914 Z= 0.149 Angle : 0.470 3.596 6426 Z= 0.256 Chirality : 0.028 0.061 357 Planarity : 0.012 0.071 777 Dihedral : 13.838 59.491 609 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.56 % Allowed : 18.49 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.22), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.17), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR r 7 PHE 0.011 0.001 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.15 ( 4851) covalent geometry : angle 0.47035 / 0.26 ( 6426) Misc. bond : bond 0.00054 / 0.03 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.138 Fit side-chains REVERT: M 6 GLN cc_start: 0.8685 (pt0) cc_final: 0.8378 (pt0) REVERT: V 6 GLN cc_start: 0.8437 (pt0) cc_final: 0.8150 (pt0) REVERT: n 8 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7634 (mm110) REVERT: w 8 GLN cc_start: 0.8276 (mm-40) cc_final: 0.5644 (pt0) outliers start: 2 outliers final: 0 residues processed: 52 average time/residue: 0.8902 time to fit residues: 47.4433 Evaluate side-chains 52 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN N 8 GLN W 8 GLN 5 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.068525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.056384 restraints weight = 8710.144| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.48 r_work: 0.2667 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.381 Angle : 0.632 3.967 6426 Z= 0.347 Chirality : 0.042 0.102 357 Planarity : 0.014 0.080 777 Dihedral : 17.470 58.869 609 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.96 % Allowed : 18.77 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.22), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.17), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 7 PHE 0.020 0.002 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00957 / 0.38 ( 4851) covalent geometry : angle 0.63196 / 0.35 ( 6426) Misc. bond : bond 0.00118 / 0.07 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.164 Fit side-chains REVERT: H 8 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: M 6 GLN cc_start: 0.8699 (pt0) cc_final: 0.8421 (pt0) REVERT: N 8 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7717 (mm110) REVERT: S 6 GLN cc_start: 0.8423 (pt0) cc_final: 0.8206 (pt0) outliers start: 7 outliers final: 1 residues processed: 53 average time/residue: 0.8505 time to fit residues: 46.2683 Evaluate side-chains 50 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain u residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 8 GLN k 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.068417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.056391 restraints weight = 8812.028| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.47 r_work: 0.2668 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.383 Angle : 0.632 3.963 6426 Z= 0.347 Chirality : 0.043 0.102 357 Planarity : 0.013 0.077 777 Dihedral : 17.310 59.049 609 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.68 % Allowed : 20.17 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.78 (0.23), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.17), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 7 PHE 0.018 0.002 PHE M 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00964 / 0.39 ( 4851) covalent geometry : angle 0.63160 / 0.35 ( 6426) Misc. bond : bond 0.00119 / 0.07 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.116 Fit side-chains REVERT: H 8 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: M 6 GLN cc_start: 0.8689 (pt0) cc_final: 0.8430 (pt0) REVERT: l 8 GLN cc_start: 0.7370 (mt0) cc_final: 0.7128 (tm-30) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.8953 time to fit residues: 46.7940 Evaluate side-chains 53 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN N 8 GLN 5 8 GLN k 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.056556 restraints weight = 8794.612| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.49 r_work: 0.2673 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.382 Angle : 0.636 3.909 6426 Z= 0.349 Chirality : 0.042 0.099 357 Planarity : 0.014 0.081 777 Dihedral : 17.494 59.734 609 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 2.24 % Allowed : 20.17 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.23), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.17), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 7 PHE 0.017 0.002 PHE B 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.38 ( 4851) covalent geometry : angle 0.63627 / 0.35 ( 6426) Misc. bond : bond 0.00114 / 0.06 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.105 Fit side-chains REVERT: H 8 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: M 6 GLN cc_start: 0.8676 (pt0) cc_final: 0.8428 (pt0) REVERT: l 8 GLN cc_start: 0.7363 (mt0) cc_final: 0.7122 (tm-30) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.8756 time to fit residues: 44.8598 Evaluate side-chains 49 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.056391 restraints weight = 8898.385| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.50 r_work: 0.2675 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.382 Angle : 0.640 4.085 6426 Z= 0.352 Chirality : 0.042 0.098 357 Planarity : 0.014 0.078 777 Dihedral : 17.553 59.878 609 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 2.24 % Allowed : 19.89 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.84 (0.23), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.17), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 7 PHE 0.032 0.002 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00961 / 0.38 ( 4851) covalent geometry : angle 0.63974 / 0.35 ( 6426) Misc. bond : bond 0.00111 / 0.06 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.171 Fit side-chains REVERT: H 8 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: M 6 GLN cc_start: 0.8691 (pt0) cc_final: 0.8441 (pt0) REVERT: l 8 GLN cc_start: 0.7360 (mt0) cc_final: 0.7127 (tm-30) REVERT: t 8 GLN cc_start: 0.8403 (mm-40) cc_final: 0.6010 (pt0) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.9016 time to fit residues: 43.4194 Evaluate side-chains 50 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 8 GLN 5 8 GLN q 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.068997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.057024 restraints weight = 8824.703| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.48 r_work: 0.2688 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.382 Angle : 0.643 4.704 6426 Z= 0.353 Chirality : 0.042 0.099 357 Planarity : 0.014 0.081 777 Dihedral : 17.599 59.996 609 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.68 % Allowed : 20.45 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.23), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.18), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR I 7 PHE 0.024 0.002 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.38 ( 4851) covalent geometry : angle 0.64323 / 0.35 ( 6426) Misc. bond : bond 0.00110 / 0.06 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.166 Fit side-chains REVERT: H 8 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: I 8 GLN cc_start: 0.7950 (mt0) cc_final: 0.7750 (mt0) REVERT: M 6 GLN cc_start: 0.8702 (pt0) cc_final: 0.8454 (pt0) REVERT: l 8 GLN cc_start: 0.7356 (mt0) cc_final: 0.7094 (tm-30) REVERT: t 8 GLN cc_start: 0.8385 (mm-40) cc_final: 0.5989 (pt0) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.8567 time to fit residues: 40.4092 Evaluate side-chains 50 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Chi-restraints excluded: chain u residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN N 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.057773 restraints weight = 8890.696| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.49 r_work: 0.2702 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 4914 Z= 0.264 Angle : 0.547 5.030 6426 Z= 0.302 Chirality : 0.036 0.082 357 Planarity : 0.013 0.077 777 Dihedral : 16.511 58.675 609 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.40 % Allowed : 20.45 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.24), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.18), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR I 7 PHE 0.020 0.002 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.27 ( 4851) covalent geometry : angle 0.54699 / 0.30 ( 6426) Misc. bond : bond 0.00079 / 0.04 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.177 Fit side-chains REVERT: H 8 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: M 6 GLN cc_start: 0.8692 (pt0) cc_final: 0.8432 (pt0) REVERT: l 8 GLN cc_start: 0.7306 (mt0) cc_final: 0.7081 (tm-30) REVERT: t 8 GLN cc_start: 0.8346 (mm-40) cc_final: 0.5803 (pt0) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.9017 time to fit residues: 43.4385 Evaluate side-chains 50 residues out of total 357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain H residue 8 GLN Chi-restraints excluded: chain U residue 8 GLN Chi-restraints excluded: chain m residue 6 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 8 GLN 5 8 GLN q 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.069056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.057121 restraints weight = 8877.693| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.48 r_work: 0.2690 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.042 4914 Z= 0.384 Angle : 0.653 4.969 6426 Z= 0.357 Chirality : 0.042 0.099 357 Planarity : 0.014 0.082 777 Dihedral : 17.653 59.744 609 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 1.68 % Allowed : 19.89 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.24), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR I 7 PHE 0.025 0.002 PHE G 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00968 / 0.39 ( 4851) covalent geometry : angle 0.65325 / 0.36 ( 6426) Misc. bond : bond 0.00115 / 0.07 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1303.82 seconds wall clock time: 22 minutes 48.33 seconds (1368.33 seconds total)