Starting phenix.real_space_refine on Tue Mar 3 12:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rtb_4996/03_2026/6rtb_4996.map" } resolution = 3.46 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= 0.000 sd= 0.001 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 2895 2.51 5 N 829 2.21 5 O 957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "I" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 460 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain breaks: 2 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "G" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "B" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "F" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Time building chain proxies: 1.16, per 1000 atoms: 0.25 Number of scatterers: 4681 At special positions: 0 Unit cell: (104.24, 132.431, 41.9584, 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 957 8.00 N 829 7.00 C 2895 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: 0.34 Conformation dependent library (CDL) restraints added in 184.9 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 17 removed outlier: 6.428A pdb=" N VAL H 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.129A pdb=" N GLY I 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR J 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR G 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER F 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.537A pdb=" N VAL H 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL G 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.779A pdb=" N ASN H 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 70 through 72 removed outlier: 6.593A pdb=" N VAL G 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.403A pdb=" N ALA H 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLN G 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA H 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA G 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN F 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 82 through 83 removed outlier: 6.722A pdb=" N VAL H 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.262A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.424A pdb=" N VAL C 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.463A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.859A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY B 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS C 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N HIS B 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.196A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.346A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.494A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 837 1.29 - 1.35: 733 1.35 - 1.42: 127 1.42 - 1.49: 864 1.49 - 1.56: 2110 Bond restraints: 4671 Sorted by residual: bond pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 bond pdb=" CA THR D 92 " pdb=" CB THR D 92 " ideal model delta sigma weight residual 1.534 1.497 0.037 1.78e-02 3.16e+03 4.32e+00 bond pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" CB VAL F 16 " pdb=" CG1 VAL F 16 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 4666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5645 1.86 - 3.72: 527 3.72 - 5.59: 86 5.59 - 7.45: 25 7.45 - 9.31: 5 Bond angle restraints: 6288 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.96 104.63 8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CG1 VAL G 16 " pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 110.80 101.49 9.31 2.20e+00 2.07e-01 1.79e+01 angle pdb=" CG1 VAL H 16 " pdb=" CB VAL H 16 " pdb=" CG2 VAL H 16 " ideal model delta sigma weight residual 110.80 101.54 9.26 2.20e+00 2.07e-01 1.77e+01 angle pdb=" C ALA F 18 " pdb=" N ALA F 19 " pdb=" CA ALA F 19 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ALA C 18 " pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 6283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2404 16.64 - 33.29: 265 33.29 - 49.93: 50 49.93 - 66.58: 8 66.58 - 83.22: 7 Dihedral angle restraints: 2734 sinusoidal: 877 harmonic: 1857 Sorted by residual: dihedral pdb=" CA ALA G 19 " pdb=" C ALA G 19 " pdb=" N GLU G 20 " pdb=" CA GLU G 20 " ideal model delta harmonic sigma weight residual 180.00 113.95 66.05 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA ALA C 19 " pdb=" C ALA C 19 " pdb=" N GLU C 20 " pdb=" CA GLU C 20 " ideal model delta harmonic sigma weight residual 180.00 128.01 51.99 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA I 19 " pdb=" C ALA I 19 " pdb=" N GLU I 20 " pdb=" CA GLU I 20 " ideal model delta harmonic sigma weight residual 180.00 128.78 51.22 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 2731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 494 0.057 - 0.115: 260 0.115 - 0.172: 68 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 839 Sorted by residual: chirality pdb=" CB THR I 81 " pdb=" CA THR I 81 " pdb=" OG1 THR I 81 " pdb=" CG2 THR I 81 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 836 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C ALA G 18 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA G 18 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA G 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 19 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ALA J 19 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA J 19 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU J 20 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 18 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ALA F 18 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA F 18 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 141 2.68 - 3.23: 3871 3.23 - 3.79: 6452 3.79 - 4.34: 8026 4.34 - 4.90: 15387 Nonbonded interactions: 33877 Sorted by model distance: nonbonded pdb=" OG SER G 87 " pdb=" O ALA F 18 " model vdw 2.122 3.040 nonbonded pdb=" O SER E 9 " pdb=" OG SER E 9 " model vdw 2.294 3.040 nonbonded pdb=" O SER C 9 " pdb=" OG SER C 9 " model vdw 2.297 3.040 nonbonded pdb=" O SER B 9 " pdb=" OG SER B 9 " model vdw 2.299 3.040 nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.301 3.040 ... (remaining 33872 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' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'B' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'C' and (resid 9 through 24 or resid 36 through 93)) selection = chain 'D' selection = (chain 'E' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'F' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'G' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'H' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'I' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'J' and (resid 9 through 24 or resid 36 through 93)) } 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: 1.370 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.980 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 4671 Z= 0.410 Angle : 1.226 9.311 6288 Z= 0.718 Chirality : 0.072 0.287 839 Planarity : 0.005 0.025 778 Dihedral : 15.078 83.221 1556 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.94 % Favored : 80.91 % Rotamer: Outliers : 2.61 % Allowed : 11.33 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % 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: -4.64 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.005 TYR D 39 HIS 0.006 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00881 ( 4671) covalent geometry : angle 1.22593 ( 6288) hydrogen bonds : bond 0.06288 ( 79) hydrogen bonds : angle 5.87479 ( 237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: H 13 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6181 (mp0) REVERT: C 43 LYS cc_start: 0.8320 (tttt) cc_final: 0.8081 (tttp) REVERT: C 80 LYS cc_start: 0.8549 (mtpt) cc_final: 0.7895 (ttmt) REVERT: I 13 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6739 (tt0) REVERT: D 43 LYS cc_start: 0.8128 (tttt) cc_final: 0.7688 (mptt) REVERT: D 80 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8189 (ttmt) REVERT: J 12 LYS cc_start: 0.7253 (mttt) cc_final: 0.5329 (tmtt) REVERT: J 13 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7572 (tt0) REVERT: J 46 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7882 (tm-30) REVERT: J 83 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7617 (mp0) REVERT: G 13 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6426 (mp0) REVERT: B 43 LYS cc_start: 0.8343 (tttt) cc_final: 0.7706 (mptt) REVERT: B 80 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8231 (ttmt) REVERT: F 13 GLU cc_start: 0.6671 (mt-10) cc_final: 0.5970 (tt0) REVERT: F 24 GLN cc_start: 0.7623 (mt0) cc_final: 0.7283 (tm-30) REVERT: F 83 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6869 (mt-10) REVERT: A 80 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8308 (ttmt) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.0829 time to fit residues: 10.6252 Evaluate side-chains 91 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 15 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN C 62 GLN C 79 GLN I 62 GLN I 79 GLN D 79 GLN J 62 GLN E 79 GLN G 62 GLN B 62 GLN B 79 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.163876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.141898 restraints weight = 6880.630| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.43 r_work: 0.4189 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4671 Z= 0.123 Angle : 0.688 5.939 6288 Z= 0.380 Chirality : 0.051 0.136 839 Planarity : 0.002 0.014 778 Dihedral : 8.581 47.002 687 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.30 % Favored : 86.70 % Rotamer: Outliers : 6.32 % Allowed : 11.98 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.05 % 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: -4.29 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4671) covalent geometry : angle 0.68771 ( 6288) hydrogen bonds : bond 0.01589 ( 79) hydrogen bonds : angle 4.65290 ( 237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.172 Fit side-chains REVERT: H 13 GLU cc_start: 0.6414 (mt-10) cc_final: 0.5953 (tt0) REVERT: H 24 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7385 (tt0) REVERT: C 43 LYS cc_start: 0.8326 (tttt) cc_final: 0.8114 (tttp) REVERT: C 80 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7833 (ttmt) REVERT: C 92 THR cc_start: 0.7793 (p) cc_final: 0.7382 (p) REVERT: I 13 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6532 (tt0) REVERT: D 80 LYS cc_start: 0.8528 (mtpt) cc_final: 0.7947 (mttp) REVERT: D 92 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7791 (p) REVERT: J 13 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7312 (tt0) REVERT: J 45 LYS cc_start: 0.8666 (tttm) cc_final: 0.7770 (mttm) REVERT: J 46 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7788 (tm-30) REVERT: J 81 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7360 (p) REVERT: J 83 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7756 (mp0) REVERT: G 13 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6093 (mp0) REVERT: B 43 LYS cc_start: 0.8360 (tttt) cc_final: 0.7541 (mptt) REVERT: B 80 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8068 (mtpp) REVERT: B 83 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7893 (mp0) REVERT: F 13 GLU cc_start: 0.6621 (mt-10) cc_final: 0.5750 (mm-30) REVERT: F 24 GLN cc_start: 0.7581 (mt0) cc_final: 0.7102 (tm-30) REVERT: F 83 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7036 (mt-10) REVERT: A 80 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7677 (ttmt) outliers start: 29 outliers final: 12 residues processed: 100 average time/residue: 0.0678 time to fit residues: 8.7434 Evaluate side-chains 82 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 0.0020 chunk 66 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.0770 chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 50 HIS C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 50 HIS A 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.158893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137625 restraints weight = 7023.128| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.44 r_work: 0.4124 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4671 Z= 0.216 Angle : 0.729 5.525 6288 Z= 0.410 Chirality : 0.052 0.200 839 Planarity : 0.002 0.009 778 Dihedral : 8.604 42.502 685 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.68 % Favored : 82.32 % Rotamer: Outliers : 7.19 % Allowed : 12.64 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -4.65 (0.30), residues: 639 helix: None (None), residues: 0 sheet: -3.53 (0.47), residues: 117 loop : -3.29 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR D 39 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4671) covalent geometry : angle 0.72895 ( 6288) hydrogen bonds : bond 0.02562 ( 79) hydrogen bonds : angle 4.44530 ( 237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.169 Fit side-chains REVERT: H 13 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6422 (mp0) REVERT: C 80 LYS cc_start: 0.8350 (mtpt) cc_final: 0.7824 (ttmt) REVERT: C 92 THR cc_start: 0.7950 (p) cc_final: 0.7561 (p) REVERT: I 13 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6913 (tt0) REVERT: D 43 LYS cc_start: 0.8430 (tttt) cc_final: 0.7738 (mptt) REVERT: D 80 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8137 (mttp) REVERT: D 83 GLU cc_start: 0.8195 (mp0) cc_final: 0.7965 (mp0) REVERT: D 92 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7944 (p) REVERT: J 12 LYS cc_start: 0.7367 (mttt) cc_final: 0.5895 (tmtt) REVERT: J 13 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7511 (tt0) REVERT: J 81 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7439 (p) REVERT: J 83 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7811 (mp0) REVERT: G 13 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6429 (mp0) REVERT: G 24 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 80 LYS cc_start: 0.8499 (mtpt) cc_final: 0.7980 (mttp) REVERT: F 13 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6077 (tt0) REVERT: F 24 GLN cc_start: 0.7474 (mt0) cc_final: 0.7136 (tm-30) REVERT: F 83 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7075 (mt-10) REVERT: A 80 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8091 (mtpp) outliers start: 33 outliers final: 19 residues processed: 101 average time/residue: 0.0562 time to fit residues: 7.4811 Evaluate side-chains 93 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 0.0470 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 16 optimal weight: 0.0010 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.168068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.146321 restraints weight = 6742.697| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.35 r_work: 0.4241 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4111 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4671 Z= 0.118 Angle : 0.613 5.760 6288 Z= 0.341 Chirality : 0.050 0.137 839 Planarity : 0.002 0.008 778 Dihedral : 7.167 37.427 685 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 5.88 % Allowed : 15.03 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.03 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR G 39 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4671) covalent geometry : angle 0.61260 ( 6288) hydrogen bonds : bond 0.01523 ( 79) hydrogen bonds : angle 4.23157 ( 237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.170 Fit side-chains REVERT: H 13 GLU cc_start: 0.6377 (mt-10) cc_final: 0.5941 (tt0) REVERT: C 80 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7821 (mtmt) REVERT: C 92 THR cc_start: 0.7910 (p) cc_final: 0.7532 (p) REVERT: I 13 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6550 (tt0) REVERT: D 43 LYS cc_start: 0.8209 (tttt) cc_final: 0.7644 (mptt) REVERT: D 80 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7966 (mttp) REVERT: D 83 GLU cc_start: 0.8112 (mp0) cc_final: 0.7769 (mp0) REVERT: D 92 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7781 (p) REVERT: J 13 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7278 (tt0) REVERT: J 83 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7802 (mp0) REVERT: E 83 GLU cc_start: 0.7913 (mp0) cc_final: 0.7698 (mp0) REVERT: B 43 LYS cc_start: 0.8248 (tttt) cc_final: 0.7637 (mptt) REVERT: B 80 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7901 (mtmt) REVERT: F 24 GLN cc_start: 0.7373 (mt0) cc_final: 0.7073 (tm-30) REVERT: F 83 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7172 (mt-10) outliers start: 27 outliers final: 14 residues processed: 99 average time/residue: 0.0529 time to fit residues: 6.9036 Evaluate side-chains 83 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 65 ASN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 50 HIS B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.155831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134255 restraints weight = 7093.819| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 2.49 r_work: 0.4065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 4671 Z= 0.291 Angle : 0.802 5.322 6288 Z= 0.450 Chirality : 0.054 0.136 839 Planarity : 0.003 0.009 778 Dihedral : 8.725 39.639 685 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.56 % Favored : 80.44 % Rotamer: Outliers : 7.63 % Allowed : 15.25 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.003 TYR D 39 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 4671) covalent geometry : angle 0.80209 ( 6288) hydrogen bonds : bond 0.03122 ( 79) hydrogen bonds : angle 4.44108 ( 237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.277 Fit side-chains REVERT: H 13 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6372 (mp0) REVERT: H 46 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: C 92 THR cc_start: 0.8121 (p) cc_final: 0.7739 (p) REVERT: I 13 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6860 (tt0) REVERT: I 83 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: D 80 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8124 (mttp) REVERT: D 92 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (p) REVERT: J 12 LYS cc_start: 0.7485 (mttt) cc_final: 0.5708 (tmtt) REVERT: J 13 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7592 (tt0) REVERT: J 81 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7522 (p) REVERT: J 83 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7679 (mp0) REVERT: G 13 GLU cc_start: 0.7118 (mp0) cc_final: 0.6858 (mp0) REVERT: G 24 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 46 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: B 80 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7923 (mttp) REVERT: B 83 GLU cc_start: 0.8097 (mp0) cc_final: 0.7894 (mp0) REVERT: F 13 GLU cc_start: 0.6650 (mt-10) cc_final: 0.5902 (tt0) REVERT: F 24 GLN cc_start: 0.7635 (mt0) cc_final: 0.7118 (tm-30) REVERT: F 83 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6982 (mt-10) outliers start: 35 outliers final: 24 residues processed: 93 average time/residue: 0.0593 time to fit residues: 7.4727 Evaluate side-chains 92 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.159244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.137612 restraints weight = 7106.587| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.47 r_work: 0.4103 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 4671 Z= 0.202 Angle : 0.722 5.290 6288 Z= 0.405 Chirality : 0.052 0.141 839 Planarity : 0.002 0.010 778 Dihedral : 8.325 39.081 685 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.06 % Favored : 82.94 % Rotamer: Outliers : 8.50 % Allowed : 15.69 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -4.31 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR D 39 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 4671) covalent geometry : angle 0.72173 ( 6288) hydrogen bonds : bond 0.02613 ( 79) hydrogen bonds : angle 4.23550 ( 237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 65 time to evaluate : 0.163 Fit side-chains REVERT: H 13 GLU cc_start: 0.6657 (mt-10) cc_final: 0.5953 (mp0) REVERT: C 92 THR cc_start: 0.8082 (p) cc_final: 0.7710 (p) REVERT: I 13 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6798 (tt0) REVERT: D 80 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8155 (mttp) REVERT: D 92 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7981 (p) REVERT: J 12 LYS cc_start: 0.7450 (mttt) cc_final: 0.5960 (tmtt) REVERT: J 13 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7506 (tt0) REVERT: J 81 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7447 (p) REVERT: J 83 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7727 (mp0) REVERT: G 13 GLU cc_start: 0.7005 (mp0) cc_final: 0.6755 (mp0) REVERT: G 24 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7747 (tm-30) REVERT: G 46 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: B 80 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7965 (mttp) REVERT: F 24 GLN cc_start: 0.7615 (mt0) cc_final: 0.7116 (tm-30) REVERT: F 83 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 83 GLU cc_start: 0.8012 (mp0) cc_final: 0.7525 (mp0) outliers start: 39 outliers final: 25 residues processed: 99 average time/residue: 0.0548 time to fit residues: 7.3427 Evaluate side-chains 94 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 0.0470 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 2.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.156386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.133644 restraints weight = 6886.417| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.64 r_work: 0.4084 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4671 Z= 0.197 Angle : 0.727 5.384 6288 Z= 0.408 Chirality : 0.053 0.179 839 Planarity : 0.002 0.010 778 Dihedral : 8.177 39.261 685 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Rotamer: Outliers : 7.84 % Allowed : 16.99 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -4.27 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR D 39 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 4671) covalent geometry : angle 0.72730 ( 6288) hydrogen bonds : bond 0.02573 ( 79) hydrogen bonds : angle 4.16907 ( 237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.171 Fit side-chains REVERT: H 13 GLU cc_start: 0.6629 (mt-10) cc_final: 0.5915 (mp0) REVERT: H 83 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7752 (mp0) REVERT: C 92 THR cc_start: 0.7925 (p) cc_final: 0.7518 (p) REVERT: I 13 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6758 (tt0) REVERT: D 80 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8121 (mttp) REVERT: D 92 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7758 (p) REVERT: J 12 LYS cc_start: 0.7300 (mttt) cc_final: 0.5815 (tmtt) REVERT: J 13 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7492 (tt0) REVERT: J 81 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7283 (p) REVERT: J 83 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7732 (mp0) REVERT: G 13 GLU cc_start: 0.6962 (mp0) cc_final: 0.6692 (mp0) REVERT: G 24 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7783 (tm-30) REVERT: G 46 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: B 80 LYS cc_start: 0.8325 (mtpt) cc_final: 0.7905 (mttp) REVERT: F 24 GLN cc_start: 0.7623 (mt0) cc_final: 0.7116 (tm-30) REVERT: F 83 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7077 (mt-10) outliers start: 36 outliers final: 23 residues processed: 94 average time/residue: 0.0545 time to fit residues: 6.9418 Evaluate side-chains 90 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.0980 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN F 65 ASN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.162214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.138901 restraints weight = 6928.210| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.66 r_work: 0.4169 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4671 Z= 0.122 Angle : 0.654 5.513 6288 Z= 0.364 Chirality : 0.051 0.143 839 Planarity : 0.002 0.011 778 Dihedral : 7.379 38.793 685 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 7.19 % Allowed : 16.12 % Favored : 76.69 % 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: -4.03 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR B 39 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4671) covalent geometry : angle 0.65414 ( 6288) hydrogen bonds : bond 0.02026 ( 79) hydrogen bonds : angle 4.01908 ( 237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.111 Fit side-chains REVERT: H 13 GLU cc_start: 0.6340 (mt-10) cc_final: 0.5848 (tt0) REVERT: H 46 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: H 83 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7742 (mp0) REVERT: C 80 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7791 (mtmt) REVERT: C 92 THR cc_start: 0.7871 (p) cc_final: 0.7467 (p) REVERT: I 13 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6456 (tt0) REVERT: D 80 LYS cc_start: 0.8410 (mtpt) cc_final: 0.7991 (mttp) REVERT: D 92 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7639 (p) REVERT: J 12 LYS cc_start: 0.7177 (mttt) cc_final: 0.5588 (tmtt) REVERT: J 13 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7361 (tt0) REVERT: J 81 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7110 (p) REVERT: J 83 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7728 (mp0) REVERT: G 13 GLU cc_start: 0.6672 (mp0) cc_final: 0.6466 (mp0) REVERT: B 80 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7877 (mttp) REVERT: F 24 GLN cc_start: 0.7531 (mt0) cc_final: 0.7049 (tm-30) REVERT: F 83 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7229 (mt-10) REVERT: A 83 GLU cc_start: 0.7912 (mp0) cc_final: 0.7653 (mp0) outliers start: 33 outliers final: 20 residues processed: 96 average time/residue: 0.0488 time to fit residues: 6.4556 Evaluate side-chains 90 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN I 62 GLN J 62 GLN E 50 HIS G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.152907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.131856 restraints weight = 7127.984| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.32 r_work: 0.4018 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 4671 Z= 0.423 Angle : 0.946 6.827 6288 Z= 0.537 Chirality : 0.061 0.197 839 Planarity : 0.004 0.014 778 Dihedral : 9.197 39.494 685 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.47 % Favored : 76.53 % Rotamer: Outliers : 7.19 % Allowed : 16.56 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.62 (0.26), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.027 0.004 TYR D 39 HIS 0.005 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00960 ( 4671) covalent geometry : angle 0.94642 ( 6288) hydrogen bonds : bond 0.04046 ( 79) hydrogen bonds : angle 4.59313 ( 237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 63 time to evaluate : 0.161 Fit side-chains REVERT: H 13 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6335 (mp0) REVERT: H 46 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: C 92 THR cc_start: 0.8125 (p) cc_final: 0.7695 (p) REVERT: I 13 GLU cc_start: 0.7528 (mt-10) cc_final: 0.6766 (tt0) REVERT: I 46 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: D 80 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8091 (mttp) REVERT: D 92 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (p) REVERT: J 12 LYS cc_start: 0.7547 (mttt) cc_final: 0.5924 (tmtt) REVERT: J 13 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7501 (tt0) REVERT: J 83 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7781 (mp0) REVERT: G 13 GLU cc_start: 0.7163 (mp0) cc_final: 0.6778 (mp0) REVERT: G 24 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7823 (tm-30) REVERT: G 46 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: B 80 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7971 (mttp) REVERT: B 92 THR cc_start: 0.7805 (p) cc_final: 0.7540 (p) REVERT: F 24 GLN cc_start: 0.7676 (mt0) cc_final: 0.7129 (tm-30) REVERT: F 83 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 83 GLU cc_start: 0.7938 (mp0) cc_final: 0.7453 (mp0) outliers start: 33 outliers final: 26 residues processed: 88 average time/residue: 0.0549 time to fit residues: 6.5207 Evaluate side-chains 94 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain A residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN I 62 GLN J 62 GLN G 62 GLN B 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.158130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.135023 restraints weight = 6855.782| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.65 r_work: 0.4097 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4671 Z= 0.146 Angle : 0.720 5.779 6288 Z= 0.399 Chirality : 0.052 0.143 839 Planarity : 0.002 0.013 778 Dihedral : 8.057 39.528 684 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Rotamer: Outliers : 5.66 % Allowed : 18.95 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.24 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4671) covalent geometry : angle 0.72009 ( 6288) hydrogen bonds : bond 0.02328 ( 79) hydrogen bonds : angle 4.25771 ( 237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.205 Fit side-chains REVERT: H 13 GLU cc_start: 0.6379 (mt-10) cc_final: 0.5885 (tt0) REVERT: H 46 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: H 83 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7757 (mp0) REVERT: C 80 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7830 (mtmt) REVERT: C 92 THR cc_start: 0.7952 (p) cc_final: 0.7540 (p) REVERT: I 13 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6461 (tt0) REVERT: D 80 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8063 (mttp) REVERT: D 92 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7621 (p) REVERT: J 12 LYS cc_start: 0.7244 (mttt) cc_final: 0.5720 (tmtt) REVERT: J 13 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7428 (tt0) REVERT: J 81 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7240 (p) REVERT: J 83 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7710 (mp0) REVERT: G 13 GLU cc_start: 0.6836 (mp0) cc_final: 0.6562 (mp0) REVERT: G 24 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 80 LYS cc_start: 0.8337 (mtpt) cc_final: 0.7910 (mttp) REVERT: F 24 GLN cc_start: 0.7613 (mt0) cc_final: 0.7092 (tm-30) REVERT: F 83 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 83 GLU cc_start: 0.7871 (mp0) cc_final: 0.7585 (mp0) outliers start: 26 outliers final: 17 residues processed: 85 average time/residue: 0.0655 time to fit residues: 7.4777 Evaluate side-chains 84 residues out of total 459 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 0.0770 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN I 62 GLN J 62 GLN B 62 GLN A 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.161708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.140432 restraints weight = 6916.006| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.31 r_work: 0.4158 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 4671 Z= 0.265 Angle : 1.278 59.137 6288 Z= 0.745 Chirality : 0.054 0.523 839 Planarity : 0.002 0.024 778 Dihedral : 8.012 39.555 684 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Rotamer: Outliers : 5.45 % Allowed : 18.08 % Favored : 76.47 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -4.21 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 4671) covalent geometry : angle 1.27772 ( 6288) hydrogen bonds : bond 0.02221 ( 79) hydrogen bonds : angle 4.25122 ( 237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.49 seconds wall clock time: 21 minutes 22.15 seconds (1282.15 seconds total)