Starting phenix.real_space_refine on Tue Feb 3 12:25:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778.map" model { file = "/net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v4f_64778/02_2026/9v4f_64778_neut.cif" } resolution = 3.52 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 1350 2.51 5 N 280 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1990 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "E" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "F" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "G" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "H" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Chain: "J" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 4, 'TRANS': 21} Time building chain proxies: 0.61, per 1000 atoms: 0.31 Number of scatterers: 1990 At special positions: 0 Unit cell: (68.968, 51.26, 41.008, 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 360 8.00 N 280 7.00 C 1350 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: 0.16 Conformation dependent library (CDL) restraints added in 76.5 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 5.839A pdb=" N LEU A 147 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU C 147 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU E 147 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU G 147 " --> pdb=" O VAL I 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 170 removed outlier: 6.642A pdb=" N VAL A 165 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE C 168 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 167 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU C 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 169 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 165 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE E 168 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA C 167 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU E 170 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 169 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL E 165 " --> pdb=" O VAL G 166 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE G 168 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA E 167 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU G 170 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER E 169 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL G 165 " --> pdb=" O VAL I 166 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE I 168 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA G 167 " --> pdb=" O ILE I 168 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LEU I 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER G 169 " --> pdb=" O LEU I 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 147 through 148 removed outlier: 5.838A pdb=" N LEU B 147 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU D 147 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU F 147 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU H 147 " --> pdb=" O VAL J 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 165 through 170 removed outlier: 6.692A pdb=" N VAL B 165 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE D 168 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA B 167 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU D 170 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER B 169 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 165 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE F 168 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA D 167 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N LEU F 170 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 169 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 165 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE H 168 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA F 167 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU H 170 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER F 169 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL H 165 " --> pdb=" O VAL J 166 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE J 168 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA H 167 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU J 170 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER H 169 " --> pdb=" O LEU J 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 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: 0.02 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 310 1.29 - 1.35: 265 1.35 - 1.42: 235 1.42 - 1.48: 335 1.48 - 1.54: 915 Bond restraints: 2060 Sorted by residual: bond pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.69e+00 bond pdb=" CB TYR F 155 " pdb=" CG TYR F 155 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.68e+00 bond pdb=" CB TYR H 155 " pdb=" CG TYR H 155 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.65e+00 bond pdb=" CB TYR J 155 " pdb=" CG TYR J 155 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.61e+00 bond pdb=" CB TYR D 155 " pdb=" CG TYR D 155 " ideal model delta sigma weight residual 1.512 1.460 0.052 2.20e-02 2.07e+03 5.60e+00 ... (remaining 2055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2632 1.22 - 2.45: 169 2.45 - 3.67: 59 3.67 - 4.90: 10 4.90 - 6.12: 10 Bond angle restraints: 2880 Sorted by residual: angle pdb=" CA TYR F 155 " pdb=" CB TYR F 155 " pdb=" CG TYR F 155 " ideal model delta sigma weight residual 113.90 107.78 6.12 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA TYR H 155 " pdb=" CB TYR H 155 " pdb=" CG TYR H 155 " ideal model delta sigma weight residual 113.90 107.80 6.10 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA TYR J 155 " pdb=" CB TYR J 155 " pdb=" CG TYR J 155 " ideal model delta sigma weight residual 113.90 107.80 6.10 1.80e+00 3.09e-01 1.15e+01 angle pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 113.90 107.81 6.09 1.80e+00 3.09e-01 1.14e+01 angle pdb=" CA TYR D 155 " pdb=" CB TYR D 155 " pdb=" CG TYR D 155 " ideal model delta sigma weight residual 113.90 107.82 6.08 1.80e+00 3.09e-01 1.14e+01 ... (remaining 2875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.19: 995 11.19 - 22.38: 105 22.38 - 33.56: 40 33.56 - 44.75: 35 44.75 - 55.94: 5 Dihedral angle restraints: 1180 sinusoidal: 430 harmonic: 750 Sorted by residual: dihedral pdb=" N TYR E 155 " pdb=" CA TYR E 155 " pdb=" CB TYR E 155 " pdb=" CG TYR E 155 " ideal model delta sinusoidal sigma weight residual -60.00 -104.64 44.64 3 1.50e+01 4.44e-03 8.03e+00 dihedral pdb=" N TYR C 155 " pdb=" CA TYR C 155 " pdb=" CB TYR C 155 " pdb=" CG TYR C 155 " ideal model delta sinusoidal sigma weight residual -60.00 -104.64 44.64 3 1.50e+01 4.44e-03 8.03e+00 dihedral pdb=" N TYR G 155 " pdb=" CA TYR G 155 " pdb=" CB TYR G 155 " pdb=" CG TYR G 155 " ideal model delta sinusoidal sigma weight residual -60.00 -104.64 44.64 3 1.50e+01 4.44e-03 8.03e+00 ... (remaining 1177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 171 0.025 - 0.050: 95 0.050 - 0.074: 24 0.074 - 0.099: 30 0.099 - 0.124: 40 Chirality restraints: 360 Sorted by residual: chirality pdb=" CB ILE G 149 " pdb=" CA ILE G 149 " pdb=" CG1 ILE G 149 " pdb=" CG2 ILE G 149 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CB ILE C 149 " pdb=" CA ILE C 149 " pdb=" CG1 ILE C 149 " pdb=" CG2 ILE C 149 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CB ILE I 149 " pdb=" CA ILE I 149 " pdb=" CG1 ILE I 149 " pdb=" CG2 ILE I 149 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 357 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 155 " -0.029 2.00e-02 2.50e+03 2.08e-02 8.68e+00 pdb=" CG TYR J 155 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR J 155 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR J 155 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 155 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR J 155 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 155 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 155 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 155 " -0.029 2.00e-02 2.50e+03 2.07e-02 8.60e+00 pdb=" CG TYR B 155 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 155 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 155 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 155 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 155 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 155 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 155 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 155 " -0.029 2.00e-02 2.50e+03 2.07e-02 8.56e+00 pdb=" CG TYR D 155 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 155 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR D 155 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 155 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 155 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 155 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 155 " -0.000 2.00e-02 2.50e+03 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 1279 3.04 - 3.51: 2017 3.51 - 3.97: 3453 3.97 - 4.44: 3334 4.44 - 4.90: 7286 Nonbonded interactions: 17369 Sorted by model distance: nonbonded pdb=" OH TYR C 158 " pdb=" OH TYR D 158 " model vdw 2.578 3.040 nonbonded pdb=" OH TYR I 158 " pdb=" OH TYR J 158 " model vdw 2.578 3.040 nonbonded pdb=" OH TYR A 158 " pdb=" OH TYR B 158 " model vdw 2.579 3.040 nonbonded pdb=" OH TYR G 158 " pdb=" OH TYR H 158 " model vdw 2.579 3.040 nonbonded pdb=" OH TYR E 158 " pdb=" OH TYR F 158 " model vdw 2.579 3.040 ... (remaining 17364 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 0.130 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 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 : 0.005 0.052 2060 Z= 0.274 Angle : 0.816 6.121 2880 Z= 0.499 Chirality : 0.051 0.124 360 Planarity : 0.015 0.064 350 Dihedral : 13.836 55.938 700 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.43 % Allowed : 25.65 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.004 TYR D 155 TRP 0.004 0.001 TRP H 156 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 2060) covalent geometry : angle 0.81587 ( 2880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.077 Fit side-chains REVERT: H 162 ASP cc_start: 0.7290 (t0) cc_final: 0.6968 (t70) REVERT: J 158 TYR cc_start: 0.5102 (m-80) cc_final: 0.4002 (m-80) REVERT: J 162 ASP cc_start: 0.7212 (t0) cc_final: 0.6918 (t70) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.0258 time to fit residues: 3.9460 Evaluate side-chains 86 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 168 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.4979 r_free = 0.4979 target = 0.220118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.205681 restraints weight = 2580.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.210662 restraints weight = 1089.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.214248 restraints weight = 559.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.216086 restraints weight = 314.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.217483 restraints weight = 198.516| |-----------------------------------------------------------------------------| r_work (final): 0.4944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2060 Z= 0.145 Angle : 0.551 3.357 2880 Z= 0.273 Chirality : 0.053 0.142 360 Planarity : 0.014 0.061 350 Dihedral : 4.618 14.576 272 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.25 % Favored : 83.75 % Rotamer: Outliers : 15.65 % Allowed : 21.30 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.54), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR J 158 TRP 0.011 0.002 TRP A 156 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2060) covalent geometry : angle 0.55140 ( 2880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 0.084 Fit side-chains REVERT: I 158 TYR cc_start: 0.5896 (m-80) cc_final: 0.5381 (m-80) REVERT: J 158 TYR cc_start: 0.5895 (m-80) cc_final: 0.5497 (m-80) outliers start: 36 outliers final: 28 residues processed: 103 average time/residue: 0.0210 time to fit residues: 2.9538 Evaluate side-chains 107 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 overall best weight: 7.4592 ------------------------------------------------------------------------------- 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 = 0.4914 r_free = 0.4914 target = 0.212406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.198481 restraints weight = 2668.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.203361 restraints weight = 1125.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.206530 restraints weight = 579.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.208627 restraints weight = 330.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.209893 restraints weight = 203.755| |-----------------------------------------------------------------------------| r_work (final): 0.4880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2060 Z= 0.203 Angle : 0.610 4.150 2880 Z= 0.304 Chirality : 0.054 0.153 360 Planarity : 0.014 0.070 350 Dihedral : 5.089 17.368 272 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 13.04 % Allowed : 24.78 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR D 155 TRP 0.010 0.003 TRP G 156 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 2060) covalent geometry : angle 0.61050 ( 2880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.077 Fit side-chains REVERT: G 158 TYR cc_start: 0.6875 (m-80) cc_final: 0.4944 (m-80) REVERT: J 158 TYR cc_start: 0.6018 (m-80) cc_final: 0.4918 (m-80) outliers start: 30 outliers final: 27 residues processed: 105 average time/residue: 0.0251 time to fit residues: 3.6101 Evaluate side-chains 106 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.4940 r_free = 0.4940 target = 0.213576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.199904 restraints weight = 2723.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.204733 restraints weight = 1155.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.207755 restraints weight = 592.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.209617 restraints weight = 340.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.211020 restraints weight = 214.345| |-----------------------------------------------------------------------------| r_work (final): 0.4915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2060 Z= 0.191 Angle : 0.600 4.459 2880 Z= 0.300 Chirality : 0.054 0.158 360 Planarity : 0.015 0.072 350 Dihedral : 4.886 16.785 270 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 13.04 % Allowed : 24.35 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.52), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.003 TYR I 158 TRP 0.009 0.002 TRP H 156 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 2060) covalent geometry : angle 0.60005 ( 2880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.075 Fit side-chains REVERT: G 158 TYR cc_start: 0.7042 (m-80) cc_final: 0.5162 (m-80) REVERT: G 165 VAL cc_start: 0.9219 (t) cc_final: 0.8890 (p) REVERT: H 165 VAL cc_start: 0.9201 (t) cc_final: 0.8970 (t) outliers start: 30 outliers final: 27 residues processed: 101 average time/residue: 0.0245 time to fit residues: 3.4265 Evaluate side-chains 107 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.4979 r_free = 0.4979 target = 0.218077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.204677 restraints weight = 2662.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.209424 restraints weight = 1112.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.212422 restraints weight = 565.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.214315 restraints weight = 323.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.215662 restraints weight = 200.778| |-----------------------------------------------------------------------------| r_work (final): 0.4958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2060 Z= 0.158 Angle : 0.589 4.599 2880 Z= 0.290 Chirality : 0.054 0.151 360 Planarity : 0.014 0.070 350 Dihedral : 4.747 16.261 270 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 12.61 % Allowed : 26.52 % Favored : 60.87 % 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: -3.74 (0.52), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR J 158 TRP 0.006 0.002 TRP G 156 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2060) covalent geometry : angle 0.58909 ( 2880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.072 Fit side-chains REVERT: C 158 TYR cc_start: 0.5857 (m-80) cc_final: 0.5586 (m-80) REVERT: D 158 TYR cc_start: 0.5756 (m-80) cc_final: 0.5405 (m-80) REVERT: G 158 TYR cc_start: 0.6973 (m-80) cc_final: 0.5008 (m-80) REVERT: G 165 VAL cc_start: 0.9193 (t) cc_final: 0.8982 (t) REVERT: I 158 TYR cc_start: 0.6105 (m-80) cc_final: 0.5154 (m-80) outliers start: 29 outliers final: 25 residues processed: 102 average time/residue: 0.0216 time to fit residues: 3.0673 Evaluate side-chains 105 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain J residue 149 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.4935 r_free = 0.4935 target = 0.211753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.199181 restraints weight = 2719.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.203670 restraints weight = 1172.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.206456 restraints weight = 607.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.208181 restraints weight = 347.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.209389 restraints weight = 214.942| |-----------------------------------------------------------------------------| r_work (final): 0.4911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2060 Z= 0.206 Angle : 0.634 6.044 2880 Z= 0.317 Chirality : 0.055 0.157 360 Planarity : 0.016 0.077 350 Dihedral : 5.010 17.753 270 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.08 % Favored : 82.92 % Rotamer: Outliers : 13.48 % Allowed : 26.09 % Favored : 60.43 % 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: -3.94 (0.52), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR J 158 TRP 0.008 0.002 TRP H 156 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 2060) covalent geometry : angle 0.63448 ( 2880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.050 Fit side-chains REVERT: C 158 TYR cc_start: 0.5898 (m-80) cc_final: 0.5261 (m-80) REVERT: D 165 VAL cc_start: 0.8989 (t) cc_final: 0.8757 (p) REVERT: E 158 TYR cc_start: 0.6597 (m-80) cc_final: 0.4832 (m-80) REVERT: F 162 ASP cc_start: 0.8117 (t0) cc_final: 0.7860 (t0) REVERT: G 158 TYR cc_start: 0.7070 (m-80) cc_final: 0.5651 (m-80) REVERT: G 165 VAL cc_start: 0.9182 (t) cc_final: 0.8958 (t) outliers start: 31 outliers final: 29 residues processed: 100 average time/residue: 0.0146 time to fit residues: 2.0308 Evaluate side-chains 110 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 160 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 13 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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 = 0.5032 r_free = 0.5032 target = 0.221789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.208411 restraints weight = 2655.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.213251 restraints weight = 1102.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.216220 restraints weight = 558.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.218305 restraints weight = 323.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.219593 restraints weight = 192.185| |-----------------------------------------------------------------------------| r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2060 Z= 0.130 Angle : 0.602 6.386 2880 Z= 0.289 Chirality : 0.054 0.147 360 Planarity : 0.014 0.071 350 Dihedral : 4.608 15.678 270 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 10.00 % Allowed : 27.39 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 158 TRP 0.004 0.001 TRP J 156 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 2060) covalent geometry : angle 0.60161 ( 2880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.074 Fit side-chains REVERT: C 165 VAL cc_start: 0.8847 (t) cc_final: 0.8641 (p) REVERT: D 165 VAL cc_start: 0.8970 (t) cc_final: 0.8716 (p) REVERT: G 158 TYR cc_start: 0.6942 (m-80) cc_final: 0.4967 (m-80) REVERT: H 158 TYR cc_start: 0.7146 (m-80) cc_final: 0.6438 (m-80) REVERT: I 158 TYR cc_start: 0.6147 (m-80) cc_final: 0.5244 (m-80) outliers start: 23 outliers final: 20 residues processed: 104 average time/residue: 0.0209 time to fit residues: 3.0520 Evaluate side-chains 104 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 0.0370 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.8066 ------------------------------------------------------------------------------- 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 = 0.5022 r_free = 0.5022 target = 0.220313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.206852 restraints weight = 2678.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.211723 restraints weight = 1111.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.214802 restraints weight = 565.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.216736 restraints weight = 319.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.218043 restraints weight = 194.231| |-----------------------------------------------------------------------------| r_work (final): 0.4999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2060 Z= 0.149 Angle : 0.619 7.875 2880 Z= 0.301 Chirality : 0.053 0.145 360 Planarity : 0.015 0.071 350 Dihedral : 4.625 15.771 270 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 10.43 % Allowed : 30.00 % Favored : 59.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR J 158 TRP 0.006 0.001 TRP H 156 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2060) covalent geometry : angle 0.61930 ( 2880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.075 Fit side-chains REVERT: C 165 VAL cc_start: 0.8927 (t) cc_final: 0.8688 (p) REVERT: D 165 VAL cc_start: 0.8997 (t) cc_final: 0.8750 (p) REVERT: E 158 TYR cc_start: 0.6512 (m-80) cc_final: 0.4570 (m-80) REVERT: G 158 TYR cc_start: 0.6965 (m-80) cc_final: 0.5395 (m-80) REVERT: I 158 TYR cc_start: 0.6168 (m-80) cc_final: 0.5231 (m-80) outliers start: 24 outliers final: 21 residues processed: 100 average time/residue: 0.0147 time to fit residues: 2.0817 Evaluate side-chains 103 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 0.0030 chunk 2 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- 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 = 0.5066 r_free = 0.5066 target = 0.225253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.211791 restraints weight = 2594.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.216634 restraints weight = 1076.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.219728 restraints weight = 546.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5039 r_free = 0.5039 target = 0.221777 restraints weight = 311.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.222899 restraints weight = 186.429| |-----------------------------------------------------------------------------| r_work (final): 0.5044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2060 Z= 0.128 Angle : 0.618 8.572 2880 Z= 0.296 Chirality : 0.053 0.140 360 Planarity : 0.014 0.067 350 Dihedral : 4.451 14.916 270 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 10.00 % Allowed : 31.30 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR J 158 TRP 0.004 0.001 TRP D 156 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2060) covalent geometry : angle 0.61822 ( 2880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.045 Fit side-chains REVERT: C 165 VAL cc_start: 0.8906 (t) cc_final: 0.8675 (p) REVERT: D 165 VAL cc_start: 0.8956 (t) cc_final: 0.8718 (p) REVERT: G 158 TYR cc_start: 0.6888 (m-80) cc_final: 0.4928 (m-80) REVERT: H 158 TYR cc_start: 0.7094 (m-80) cc_final: 0.6358 (m-80) REVERT: I 158 TYR cc_start: 0.6145 (m-80) cc_final: 0.5211 (m-80) REVERT: J 158 TYR cc_start: 0.6216 (m-80) cc_final: 0.5846 (m-80) outliers start: 23 outliers final: 20 residues processed: 99 average time/residue: 0.0186 time to fit residues: 2.5581 Evaluate side-chains 104 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 0.0870 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- 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 = 0.5134 r_free = 0.5134 target = 0.240483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.223523 restraints weight = 2532.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.228889 restraints weight = 1046.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.232403 restraints weight = 535.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.234367 restraints weight = 307.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.235913 restraints weight = 199.322| |-----------------------------------------------------------------------------| r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2060 Z= 0.114 Angle : 0.606 8.453 2880 Z= 0.290 Chirality : 0.052 0.136 360 Planarity : 0.013 0.062 350 Dihedral : 4.151 13.468 270 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % Rotamer: Outliers : 8.26 % Allowed : 32.61 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR J 158 TRP 0.004 0.001 TRP D 156 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2060) covalent geometry : angle 0.60559 ( 2880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.045 Fit side-chains REVERT: C 165 VAL cc_start: 0.8951 (t) cc_final: 0.8738 (p) REVERT: D 165 VAL cc_start: 0.8980 (t) cc_final: 0.8738 (p) REVERT: G 158 TYR cc_start: 0.6786 (m-80) cc_final: 0.4959 (m-80) REVERT: I 158 TYR cc_start: 0.6152 (m-80) cc_final: 0.5298 (m-80) REVERT: J 158 TYR cc_start: 0.6088 (m-80) cc_final: 0.5557 (m-80) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0159 time to fit residues: 2.1522 Evaluate side-chains 100 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 160 THR Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 168 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 16 optimal weight: 0.0470 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 2.2684 ------------------------------------------------------------------------------- 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 = 0.5148 r_free = 0.5148 target = 0.241519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.224983 restraints weight = 2556.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.230284 restraints weight = 1071.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.233817 restraints weight = 557.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.236020 restraints weight = 322.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.237537 restraints weight = 202.771| |-----------------------------------------------------------------------------| r_work (final): 0.5099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2060 Z= 0.112 Angle : 0.622 9.400 2880 Z= 0.292 Chirality : 0.052 0.134 360 Planarity : 0.013 0.060 350 Dihedral : 4.115 13.157 270 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 7.83 % Allowed : 33.04 % Favored : 59.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.53), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR J 158 TRP 0.004 0.001 TRP D 156 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 2060) covalent geometry : angle 0.62179 ( 2880) =============================================================================== Job complete usr+sys time: 477.20 seconds wall clock time: 8 minutes 53.73 seconds (533.73 seconds total)