Starting phenix.real_space_refine on Thu Aug 6 09:40:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfz_43195/08_2026/8vfz_43195.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 342 5.49 5 S 28 5.16 5 C 8336 2.51 5 N 2764 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14906 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 3.40, per 1000 atoms: 0.23 Number of scatterers: 14906 At special positions: 0 Unit cell: (81.84, 137.28, 199.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 342 15.00 O 3436 8.00 N 2764 7.00 C 8336 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: 1.08 Conformation dependent library (CDL) restraints added in 454.0 milliseconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 66.8% alpha, 2.8% beta 171 base pairs and 289 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.522A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.744A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 251 removed outlier: 3.625A pdb=" N GLY O 251 " --> pdb=" O PRO O 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 248 through 251' Processing helix chain 'P' and resid 174 through 186 Processing helix chain 'P' and resid 192 through 204 Processing helix chain 'P' and resid 205 through 209 removed outlier: 3.826A pdb=" N GLN P 209 " --> pdb=" O TYR P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 225 removed outlier: 3.822A pdb=" N ASN P 216 " --> pdb=" O GLN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 251 removed outlier: 3.848A pdb=" N GLY P 251 " --> pdb=" O PRO P 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 248 through 251' Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.135A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.515A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.112A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.799A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.579A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.638A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 228 through 231 Processing sheet with id=AA2, first strand: chain 'P' and resid 228 through 231 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.428A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.892A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.175A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 478 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 289 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2587 1.33 - 1.45: 5293 1.45 - 1.57: 7287 1.57 - 1.69: 682 1.69 - 1.81: 46 Bond restraints: 15895 Sorted by residual: bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.91e+01 bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.72e+01 bond pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.68e+01 bond pdb=" C1' DT J 35 " pdb=" N1 DT J 35 " ideal model delta sigma weight residual 1.468 1.540 -0.072 1.40e-02 5.10e+03 2.67e+01 bond pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.60e+01 ... (remaining 15890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 20863 1.41 - 2.81: 1677 2.81 - 4.22: 365 4.22 - 5.62: 21 5.62 - 7.03: 2 Bond angle restraints: 22928 Sorted by residual: angle pdb=" O4' DT J 126 " pdb=" C1' DT J 126 " pdb=" N1 DT J 126 " ideal model delta sigma weight residual 108.00 112.29 -4.29 7.00e-01 2.04e+00 3.75e+01 angle pdb=" O4' DG I 36 " pdb=" C1' DG I 36 " pdb=" N9 DG I 36 " ideal model delta sigma weight residual 108.00 111.57 -3.57 7.00e-01 2.04e+00 2.61e+01 angle pdb=" O4' DC J 56 " pdb=" C4' DC J 56 " pdb=" C3' DC J 56 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 29 " pdb=" C4 DT I 29 " pdb=" O4 DT I 29 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 22923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 7098 32.42 - 64.85: 1609 64.85 - 97.27: 46 97.27 - 129.69: 0 129.69 - 162.12: 2 Dihedral angle restraints: 8755 sinusoidal: 5893 harmonic: 2862 Sorted by residual: dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 57.88 162.12 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1642 0.036 - 0.071: 485 0.071 - 0.107: 150 0.107 - 0.142: 208 0.142 - 0.178: 78 Chirality restraints: 2563 Sorted by residual: chirality pdb=" C3' DA I 35 " pdb=" C4' DA I 35 " pdb=" O3' DA I 35 " pdb=" C2' DA I 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.90e-01 chirality pdb=" C3' DA I 134 " pdb=" C4' DA I 134 " pdb=" O3' DA I 134 " pdb=" C2' DA I 134 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" C3' DG I 113 " pdb=" C4' DG I 113 " pdb=" O3' DG I 113 " pdb=" C2' DG I 113 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2560 not shown) Planarity restraints: 1719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 237 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO P 238 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO P 238 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 238 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO O 238 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.032 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " 0.001 2.00e-02 2.50e+03 ... (remaining 1716 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 183 2.63 - 3.20: 12511 3.20 - 3.77: 28290 3.77 - 4.33: 36387 4.33 - 4.90: 52114 Nonbonded interactions: 129485 Sorted by model distance: nonbonded pdb=" OP1 DA I 144 " pdb=" OG SER H 32 " model vdw 2.063 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.073 3.040 nonbonded pdb=" OP1 DG J 143 " pdb=" OG1 THR A 45 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN F 27 " pdb=" NH1 ARG F 55 " model vdw 2.235 3.120 ... (remaining 129480 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'O' selection = chain 'P' } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.007 0.076 15895 Z= 0.597 Angle : 0.832 7.031 22928 Z= 0.735 Chirality : 0.056 0.178 2563 Planarity : 0.005 0.094 1719 Dihedral : 25.927 162.118 6911 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.97 % Favored : 97.72 % Rotamer: Outliers : 1.20 % Allowed : 1.92 % Favored : 96.89 % 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: 3.06 (0.28), residues: 964 helix: 3.30 (0.21), residues: 622 sheet: -1.64 (0.94), residues: 24 loop : -0.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 265 TYR 0.007 0.001 TYR B 72 PHE 0.008 0.001 PHE P 224 TRP 0.013 0.002 TRP P 214 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.60 (15895) covalent geometry : angle 0.83226 / 0.74 (22928) hydrogen bonds : bond 0.09641 / 6.13 ( 895) hydrogen bonds : angle 3.61872 / 3.05 ( 2235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 450 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 204 PHE cc_start: 0.9280 (m-80) cc_final: 0.9022 (m-80) REVERT: O 260 LEU cc_start: 0.4439 (OUTLIER) cc_final: 0.3683 (tt) REVERT: P 175 TYR cc_start: 0.4490 (m-80) cc_final: 0.3497 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9050 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8070 (mm-40) REVERT: G 34 LEU cc_start: 0.9644 (mt) cc_final: 0.9435 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8386 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9326 (mt) REVERT: G 84 GLN cc_start: 0.9004 (tp40) cc_final: 0.8796 (tp-100) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9291 (tp) REVERT: G 88 ARG cc_start: 0.8798 (mmt180) cc_final: 0.7981 (mtp180) REVERT: G 100 VAL cc_start: 0.9270 (t) cc_final: 0.8997 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8800 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.8020 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8624 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8689 (mt) REVERT: A 101 VAL cc_start: 0.9237 (t) cc_final: 0.8985 (t) REVERT: A 105 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8506 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8439 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8496 (m-30) REVERT: B 70 VAL cc_start: 0.9680 (t) cc_final: 0.9342 (m) REVERT: B 87 VAL cc_start: 0.9811 (t) cc_final: 0.9592 (t) REVERT: B 91 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9214 (ptmm) REVERT: C 38 ASN cc_start: 0.8671 (m110) cc_final: 0.8302 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.8007 (t80) REVERT: C 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9479 (tp) REVERT: C 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8564 (t0) REVERT: C 92 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8289 (mt-10) REVERT: D 62 MET cc_start: 0.9190 (mmm) cc_final: 0.8918 (mmm) REVERT: D 85 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9058 (mmmt) REVERT: D 87 SER cc_start: 0.9418 (m) cc_final: 0.8458 (p) REVERT: E 48 LEU cc_start: 0.9319 (mt) cc_final: 0.8955 (mt) REVERT: E 60 LEU cc_start: 0.9209 (mt) cc_final: 0.7991 (mp) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8249 (tm-30) REVERT: E 109 LEU cc_start: 0.9645 (mt) cc_final: 0.9150 (mm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8877 (mp10) REVERT: F 64 ASN cc_start: 0.9122 (m-40) cc_final: 0.8449 (m110) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8701 (m-30) REVERT: F 84 MET cc_start: 0.9140 (mmm) cc_final: 0.8936 (tpp) REVERT: F 85 ASP cc_start: 0.9098 (m-30) cc_final: 0.8802 (t0) REVERT: F 91 LYS cc_start: 0.9430 (ttpt) cc_final: 0.9111 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8639 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8484 (t0) REVERT: H 87 SER cc_start: 0.9196 (m) cc_final: 0.8926 (t) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8211 (p) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8341 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8788 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.1492 time to fit residues: 94.6630 Evaluate side-chains 293 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 290 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 209 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 GLN G 68 ASN G 89 ASN B 75 HIS B 93 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.078269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056859 restraints weight = 85620.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.058175 restraints weight = 45523.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.058982 restraints weight = 30331.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.059558 restraints weight = 23814.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059921 restraints weight = 20439.917| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15895 Z= 0.194 Angle : 0.741 10.480 22928 Z= 0.437 Chirality : 0.048 0.278 2563 Planarity : 0.006 0.094 1719 Dihedral : 29.829 164.703 4918 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.28 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 3.47 % Favored : 96.05 % 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: 2.22 (0.27), residues: 964 helix: 2.45 (0.20), residues: 626 sheet: -1.15 (1.04), residues: 24 loop : -0.33 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 213 TYR 0.033 0.002 TYR G 39 PHE 0.018 0.002 PHE G 25 TRP 0.022 0.003 TRP P 214 HIS 0.006 0.001 HIS P 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.19 (15895) covalent geometry : angle 0.74091 / 0.44 (22928) hydrogen bonds : bond 0.05844 / 3.77 ( 895) hydrogen bonds : angle 3.49872 / 3.06 ( 2235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 204 PHE cc_start: 0.9218 (m-80) cc_final: 0.8975 (m-80) REVERT: O 215 GLN cc_start: 0.9447 (pt0) cc_final: 0.9204 (pt0) REVERT: O 230 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7302 (mtpp) REVERT: P 181 MET cc_start: 0.3811 (tpt) cc_final: 0.3068 (mmt) REVERT: G 34 LEU cc_start: 0.9654 (mt) cc_final: 0.9439 (mt) REVERT: G 58 LEU cc_start: 0.9679 (mm) cc_final: 0.9378 (mm) REVERT: G 64 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.8932 (pm20) REVERT: G 83 LEU cc_start: 0.9580 (mt) cc_final: 0.9352 (mt) REVERT: G 84 GLN cc_start: 0.9020 (tp40) cc_final: 0.8573 (tp-100) REVERT: G 87 ILE cc_start: 0.9549 (mt) cc_final: 0.9250 (tp) REVERT: G 88 ARG cc_start: 0.8873 (mmt180) cc_final: 0.7910 (mtp180) REVERT: G 100 VAL cc_start: 0.9318 (t) cc_final: 0.8857 (p) REVERT: G 107 VAL cc_start: 0.8992 (m) cc_final: 0.8674 (p) REVERT: A 50 GLU cc_start: 0.9420 (mt-10) cc_final: 0.8806 (mt-10) REVERT: A 51 ILE cc_start: 0.8322 (mt) cc_final: 0.7974 (mt) REVERT: A 53 ARG cc_start: 0.9505 (ptm-80) cc_final: 0.9304 (ptm160) REVERT: A 87 SER cc_start: 0.8947 (p) cc_final: 0.8395 (t) REVERT: A 90 MET cc_start: 0.8869 (mpp) cc_final: 0.8538 (mmm) REVERT: A 105 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8561 (tm-30) REVERT: A 126 LEU cc_start: 0.9532 (mm) cc_final: 0.9126 (mm) REVERT: A 130 ILE cc_start: 0.9539 (mm) cc_final: 0.9264 (mm) REVERT: B 39 ARG cc_start: 0.9251 (mmt-90) cc_final: 0.8664 (tpp-160) REVERT: B 49 LEU cc_start: 0.9513 (mm) cc_final: 0.9017 (tp) REVERT: B 63 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8469 (mp0) REVERT: B 64 ASN cc_start: 0.8960 (m-40) cc_final: 0.8745 (t0) REVERT: B 78 ARG cc_start: 0.8507 (mtm110) cc_final: 0.7985 (mtm110) REVERT: B 84 MET cc_start: 0.9326 (mpp) cc_final: 0.9024 (mpp) REVERT: C 50 TYR cc_start: 0.8336 (t80) cc_final: 0.7827 (t80) REVERT: C 90 ASP cc_start: 0.8660 (t0) cc_final: 0.8423 (t0) REVERT: D 62 MET cc_start: 0.9142 (mmm) cc_final: 0.8566 (mmm) REVERT: D 85 LYS cc_start: 0.9429 (mtpt) cc_final: 0.9061 (mmmt) REVERT: E 48 LEU cc_start: 0.9244 (mt) cc_final: 0.8640 (mt) REVERT: E 73 GLU cc_start: 0.9268 (pt0) cc_final: 0.8975 (pt0) REVERT: E 79 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8668 (ttpp) REVERT: E 120 MET cc_start: 0.8812 (mmm) cc_final: 0.8462 (mmm) REVERT: F 44 LYS cc_start: 0.9006 (tptm) cc_final: 0.8119 (tptm) REVERT: F 64 ASN cc_start: 0.8924 (m-40) cc_final: 0.8452 (m-40) REVERT: F 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8788 (t0) REVERT: F 87 VAL cc_start: 0.9717 (t) cc_final: 0.9471 (t) REVERT: F 91 LYS cc_start: 0.9447 (ttpt) cc_final: 0.9097 (ptpt) REVERT: H 34 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8971 (mmmm) REVERT: H 52 THR cc_start: 0.8485 (t) cc_final: 0.8111 (t) REVERT: H 59 MET cc_start: 0.8982 (tpp) cc_final: 0.8500 (tpp) REVERT: H 68 ASP cc_start: 0.8888 (t0) cc_final: 0.8415 (t0) REVERT: H 69 ILE cc_start: 0.9048 (mm) cc_final: 0.8750 (mm) REVERT: H 105 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8887 (mm-30) REVERT: H 113 GLU cc_start: 0.9435 (mm-30) cc_final: 0.8983 (mm-30) outliers start: 4 outliers final: 1 residues processed: 352 average time/residue: 0.1385 time to fit residues: 69.5842 Evaluate side-chains 262 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 30 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 210 ASN ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.076849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055798 restraints weight = 83872.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057048 restraints weight = 43950.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057942 restraints weight = 29202.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058433 restraints weight = 22888.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.058815 restraints weight = 19932.390| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15895 Z= 0.200 Angle : 0.724 8.637 22928 Z= 0.428 Chirality : 0.047 0.285 2563 Planarity : 0.007 0.108 1719 Dihedral : 30.202 163.934 4918 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.49 % Favored : 97.20 % Rotamer: Outliers : 0.60 % Allowed : 3.47 % Favored : 95.93 % 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: 1.68 (0.27), residues: 964 helix: 1.97 (0.20), residues: 628 sheet: -1.27 (1.01), residues: 24 loop : -0.45 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 77 TYR 0.027 0.002 TYR F 88 PHE 0.019 0.002 PHE G 25 TRP 0.018 0.003 TRP P 214 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.20 (15895) covalent geometry : angle 0.72435 / 0.43 (22928) hydrogen bonds : bond 0.05739 / 3.72 ( 895) hydrogen bonds : angle 3.55664 / 3.19 ( 2235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 329 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 175 TYR cc_start: 0.4480 (m-80) cc_final: 0.4157 (m-80) REVERT: P 181 MET cc_start: 0.3910 (tpt) cc_final: 0.3148 (mmt) REVERT: P 201 MET cc_start: 0.0426 (mmt) cc_final: 0.0172 (mmt) REVERT: G 24 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8483 (mp10) REVERT: G 58 LEU cc_start: 0.9658 (mm) cc_final: 0.9336 (mm) REVERT: G 78 ILE cc_start: 0.9029 (mm) cc_final: 0.8795 (mm) REVERT: G 84 GLN cc_start: 0.9052 (tp40) cc_final: 0.8839 (tp-100) REVERT: G 88 ARG cc_start: 0.8854 (mmt180) cc_final: 0.7713 (mtp180) REVERT: G 94 ASN cc_start: 0.9287 (t0) cc_final: 0.9012 (m-40) REVERT: G 99 ARG cc_start: 0.8430 (mtt90) cc_final: 0.8216 (mtt90) REVERT: A 50 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9167 (tt0) REVERT: A 53 ARG cc_start: 0.9494 (ptm-80) cc_final: 0.9188 (ptm160) REVERT: A 61 LEU cc_start: 0.8837 (mt) cc_final: 0.8310 (mt) REVERT: A 73 GLU cc_start: 0.8190 (tt0) cc_final: 0.7772 (tt0) REVERT: A 87 SER cc_start: 0.9027 (p) cc_final: 0.8280 (t) REVERT: A 90 MET cc_start: 0.8978 (mpp) cc_final: 0.8696 (mpp) REVERT: A 105 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8521 (tm-30) REVERT: A 130 ILE cc_start: 0.9541 (mm) cc_final: 0.9281 (mm) REVERT: B 25 ASN cc_start: 0.7343 (m-40) cc_final: 0.7134 (m110) REVERT: B 49 LEU cc_start: 0.9533 (mm) cc_final: 0.9031 (tp) REVERT: B 66 ILE cc_start: 0.9813 (mm) cc_final: 0.9581 (pt) REVERT: B 78 ARG cc_start: 0.8787 (mtm110) cc_final: 0.8071 (mtm110) REVERT: B 84 MET cc_start: 0.9351 (mpp) cc_final: 0.9082 (mpp) REVERT: C 78 ILE cc_start: 0.8435 (mm) cc_final: 0.8204 (tp) REVERT: C 87 ILE cc_start: 0.9319 (mt) cc_final: 0.9114 (mt) REVERT: C 90 ASP cc_start: 0.8665 (t0) cc_final: 0.8408 (t0) REVERT: C 92 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8634 (mm-30) REVERT: C 94 ASN cc_start: 0.9474 (t0) cc_final: 0.9235 (m-40) REVERT: D 62 MET cc_start: 0.9165 (mmm) cc_final: 0.8793 (mmm) REVERT: D 85 LYS cc_start: 0.9481 (mtpt) cc_final: 0.9111 (mmmt) REVERT: E 50 GLU cc_start: 0.9143 (tp30) cc_final: 0.8867 (tp30) REVERT: E 74 ILE cc_start: 0.9372 (mt) cc_final: 0.9125 (mt) REVERT: E 77 ASP cc_start: 0.9587 (m-30) cc_final: 0.9375 (m-30) REVERT: E 120 MET cc_start: 0.8876 (mmm) cc_final: 0.8596 (mmm) REVERT: F 64 ASN cc_start: 0.8864 (m-40) cc_final: 0.8537 (m110) REVERT: F 68 ASP cc_start: 0.8950 (m-30) cc_final: 0.8528 (m-30) REVERT: F 84 MET cc_start: 0.9377 (tpt) cc_final: 0.8805 (tpp) REVERT: F 91 LYS cc_start: 0.9454 (ttpt) cc_final: 0.9122 (ptpt) REVERT: H 34 LYS cc_start: 0.9219 (mmmt) cc_final: 0.9011 (mmmm) REVERT: H 46 LYS cc_start: 0.9451 (ptpp) cc_final: 0.8777 (ptpp) REVERT: H 49 HIS cc_start: 0.8982 (m-70) cc_final: 0.8384 (m-70) REVERT: H 59 MET cc_start: 0.9169 (tpp) cc_final: 0.8589 (tpp) REVERT: H 63 ASN cc_start: 0.9195 (m-40) cc_final: 0.8894 (m110) REVERT: H 68 ASP cc_start: 0.8963 (t0) cc_final: 0.8613 (t0) REVERT: H 69 ILE cc_start: 0.9050 (mm) cc_final: 0.8689 (mm) REVERT: H 109 HIS cc_start: 0.8969 (m-70) cc_final: 0.8427 (m-70) REVERT: H 113 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9016 (mm-30) outliers start: 5 outliers final: 1 residues processed: 331 average time/residue: 0.1340 time to fit residues: 63.5790 Evaluate side-chains 269 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 43 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 210 ASN ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.076268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055279 restraints weight = 84640.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056543 restraints weight = 44532.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057402 restraints weight = 29302.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057943 restraints weight = 22859.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.058246 restraints weight = 19765.253| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15895 Z= 0.189 Angle : 0.701 7.980 22928 Z= 0.414 Chirality : 0.046 0.289 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.405 163.531 4918 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.70 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 1.62 (0.27), residues: 964 helix: 1.89 (0.20), residues: 628 sheet: -1.07 (1.12), residues: 24 loop : -0.37 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.023 0.002 TYR G 39 PHE 0.019 0.002 PHE F 61 TRP 0.013 0.002 TRP O 214 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.19 (15895) covalent geometry : angle 0.70106 / 0.41 (22928) hydrogen bonds : bond 0.05453 / 3.52 ( 895) hydrogen bonds : angle 3.52605 / 3.09 ( 2235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.3911 (tpt) cc_final: 0.3190 (mmt) REVERT: G 25 PHE cc_start: 0.8536 (m-10) cc_final: 0.8302 (m-10) REVERT: G 58 LEU cc_start: 0.9648 (mm) cc_final: 0.9327 (mm) REVERT: G 68 ASN cc_start: 0.9667 (m-40) cc_final: 0.9467 (m110) REVERT: G 78 ILE cc_start: 0.9030 (mm) cc_final: 0.8817 (mm) REVERT: G 84 GLN cc_start: 0.8973 (tp40) cc_final: 0.8586 (tp-100) REVERT: G 87 ILE cc_start: 0.9576 (mt) cc_final: 0.9283 (mt) REVERT: G 88 ARG cc_start: 0.8839 (mmt180) cc_final: 0.7614 (mtp180) REVERT: G 94 ASN cc_start: 0.9236 (t0) cc_final: 0.8965 (m-40) REVERT: G 100 VAL cc_start: 0.9343 (p) cc_final: 0.8964 (p) REVERT: A 51 ILE cc_start: 0.8435 (mt) cc_final: 0.8003 (mt) REVERT: A 60 LEU cc_start: 0.9283 (mm) cc_final: 0.9066 (mm) REVERT: A 61 LEU cc_start: 0.8723 (mt) cc_final: 0.7993 (mt) REVERT: A 87 SER cc_start: 0.9084 (p) cc_final: 0.8558 (t) REVERT: A 90 MET cc_start: 0.8993 (mpp) cc_final: 0.8626 (mmm) REVERT: A 105 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8423 (tm-30) REVERT: A 130 ILE cc_start: 0.9553 (mm) cc_final: 0.9301 (mm) REVERT: B 39 ARG cc_start: 0.9120 (mmt-90) cc_final: 0.8784 (tpp-160) REVERT: B 49 LEU cc_start: 0.9535 (mm) cc_final: 0.9052 (tp) REVERT: B 78 ARG cc_start: 0.9101 (mtm110) cc_final: 0.8567 (mtm110) REVERT: B 84 MET cc_start: 0.9361 (mpp) cc_final: 0.9107 (mpp) REVERT: C 78 ILE cc_start: 0.8606 (mm) cc_final: 0.8347 (tp) REVERT: C 90 ASP cc_start: 0.8701 (t0) cc_final: 0.8436 (t0) REVERT: C 92 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8757 (mt-10) REVERT: C 94 ASN cc_start: 0.9486 (t0) cc_final: 0.9229 (m-40) REVERT: D 62 MET cc_start: 0.9219 (mmm) cc_final: 0.8886 (mmm) REVERT: D 101 LEU cc_start: 0.9166 (tt) cc_final: 0.8927 (tt) REVERT: E 50 GLU cc_start: 0.9155 (tp30) cc_final: 0.8822 (tp30) REVERT: E 60 LEU cc_start: 0.9225 (mm) cc_final: 0.8852 (mm) REVERT: E 74 ILE cc_start: 0.9389 (mt) cc_final: 0.9089 (mt) REVERT: E 77 ASP cc_start: 0.9573 (m-30) cc_final: 0.9370 (m-30) REVERT: E 120 MET cc_start: 0.8960 (mmm) cc_final: 0.8231 (mmm) REVERT: F 49 LEU cc_start: 0.9417 (mm) cc_final: 0.8903 (mt) REVERT: F 63 GLU cc_start: 0.9323 (pt0) cc_final: 0.9099 (pt0) REVERT: F 64 ASN cc_start: 0.8914 (m-40) cc_final: 0.8666 (m110) REVERT: F 84 MET cc_start: 0.9301 (tpt) cc_final: 0.8884 (tpp) REVERT: F 87 VAL cc_start: 0.9693 (t) cc_final: 0.9485 (t) REVERT: F 91 LYS cc_start: 0.9460 (ttpt) cc_final: 0.9162 (ptpt) REVERT: H 46 LYS cc_start: 0.9448 (ptpp) cc_final: 0.8817 (ptpp) REVERT: H 47 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8968 (tm-30) REVERT: H 49 HIS cc_start: 0.8976 (m-70) cc_final: 0.8572 (m90) REVERT: H 59 MET cc_start: 0.9053 (tpp) cc_final: 0.8679 (tpp) REVERT: H 68 ASP cc_start: 0.8887 (t0) cc_final: 0.8597 (t0) REVERT: H 69 ILE cc_start: 0.9014 (mm) cc_final: 0.8584 (mm) REVERT: H 113 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8488 (mm-30) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1166 time to fit residues: 53.1468 Evaluate side-chains 265 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 210 ASN ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054723 restraints weight = 87134.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055894 restraints weight = 46006.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056728 restraints weight = 30969.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057218 restraints weight = 24466.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057401 restraints weight = 21130.855| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15895 Z= 0.174 Angle : 0.697 7.885 22928 Z= 0.411 Chirality : 0.045 0.289 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.504 162.971 4918 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.70 % Favored : 96.99 % Rotamer: Outliers : 0.12 % Allowed : 2.04 % Favored : 97.84 % 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: 1.52 (0.27), residues: 964 helix: 1.79 (0.20), residues: 628 sheet: -1.14 (1.07), residues: 24 loop : -0.38 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.040 0.003 TYR P 175 PHE 0.018 0.002 PHE F 61 TRP 0.014 0.002 TRP O 214 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (15895) covalent geometry : angle 0.69737 / 0.41 (22928) hydrogen bonds : bond 0.05131 / 3.31 ( 895) hydrogen bonds : angle 3.45315 / 3.02 ( 2235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.3886 (tpt) cc_final: 0.3212 (mmt) REVERT: G 38 ASN cc_start: 0.9109 (t0) cc_final: 0.8890 (t0) REVERT: G 84 GLN cc_start: 0.8967 (tp40) cc_final: 0.8625 (tp-100) REVERT: G 87 ILE cc_start: 0.9573 (mt) cc_final: 0.9288 (mt) REVERT: G 88 ARG cc_start: 0.8859 (mmt180) cc_final: 0.7579 (mtp180) REVERT: G 94 ASN cc_start: 0.9242 (t0) cc_final: 0.9034 (m-40) REVERT: G 100 VAL cc_start: 0.9387 (p) cc_final: 0.9000 (p) REVERT: A 51 ILE cc_start: 0.8338 (mt) cc_final: 0.7956 (mt) REVERT: A 61 LEU cc_start: 0.8675 (mt) cc_final: 0.7979 (mt) REVERT: A 87 SER cc_start: 0.9078 (p) cc_final: 0.8573 (t) REVERT: A 89 VAL cc_start: 0.9023 (t) cc_final: 0.8772 (t) REVERT: A 90 MET cc_start: 0.9017 (mpp) cc_final: 0.8615 (mmm) REVERT: A 105 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8445 (tm-30) REVERT: A 130 ILE cc_start: 0.9523 (mm) cc_final: 0.9253 (mm) REVERT: B 39 ARG cc_start: 0.9024 (mmt-90) cc_final: 0.8632 (tpp-160) REVERT: B 49 LEU cc_start: 0.9511 (mm) cc_final: 0.9049 (tp) REVERT: B 68 ASP cc_start: 0.9029 (m-30) cc_final: 0.8802 (m-30) REVERT: B 78 ARG cc_start: 0.9128 (mtm110) cc_final: 0.8402 (mtm110) REVERT: B 84 MET cc_start: 0.9407 (mpp) cc_final: 0.9107 (mpp) REVERT: C 87 ILE cc_start: 0.9308 (mt) cc_final: 0.9104 (mt) REVERT: C 90 ASP cc_start: 0.8685 (t0) cc_final: 0.8382 (t0) REVERT: C 92 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8785 (mt-10) REVERT: C 94 ASN cc_start: 0.9486 (t0) cc_final: 0.9226 (m-40) REVERT: D 62 MET cc_start: 0.9129 (mmm) cc_final: 0.8760 (mmm) REVERT: D 83 TYR cc_start: 0.8326 (m-10) cc_final: 0.7626 (m-10) REVERT: D 85 LYS cc_start: 0.9502 (mtpt) cc_final: 0.9027 (mmmt) REVERT: D 101 LEU cc_start: 0.9165 (tt) cc_final: 0.8945 (tt) REVERT: E 48 LEU cc_start: 0.9333 (mt) cc_final: 0.9125 (mt) REVERT: E 50 GLU cc_start: 0.9133 (tp30) cc_final: 0.8791 (tp30) REVERT: E 60 LEU cc_start: 0.9176 (mm) cc_final: 0.8755 (mm) REVERT: E 74 ILE cc_start: 0.9408 (mt) cc_final: 0.9111 (mt) REVERT: E 77 ASP cc_start: 0.9583 (m-30) cc_final: 0.9365 (m-30) REVERT: E 90 MET cc_start: 0.9488 (mmp) cc_final: 0.9276 (mmp) REVERT: E 93 GLN cc_start: 0.8766 (tt0) cc_final: 0.8511 (tt0) REVERT: E 120 MET cc_start: 0.8988 (mmm) cc_final: 0.8480 (mmm) REVERT: F 63 GLU cc_start: 0.9326 (pt0) cc_final: 0.8841 (pp20) REVERT: F 64 ASN cc_start: 0.9054 (m-40) cc_final: 0.7672 (m-40) REVERT: F 68 ASP cc_start: 0.8888 (m-30) cc_final: 0.8660 (m-30) REVERT: F 88 TYR cc_start: 0.8919 (m-10) cc_final: 0.8609 (m-10) REVERT: H 46 LYS cc_start: 0.9493 (ptpp) cc_final: 0.9198 (mmtt) REVERT: H 47 GLN cc_start: 0.9233 (tm-30) cc_final: 0.8844 (tm-30) REVERT: H 49 HIS cc_start: 0.8963 (m-70) cc_final: 0.8562 (m90) REVERT: H 59 MET cc_start: 0.9065 (tpp) cc_final: 0.8645 (tpp) REVERT: H 68 ASP cc_start: 0.8853 (t0) cc_final: 0.8598 (t0) REVERT: H 69 ILE cc_start: 0.9006 (mm) cc_final: 0.8595 (mm) REVERT: H 82 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8680 (m90) REVERT: H 109 HIS cc_start: 0.8779 (m-70) cc_final: 0.8227 (m-70) REVERT: H 113 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8750 (mm-30) outliers start: 1 outliers final: 0 residues processed: 312 average time/residue: 0.1267 time to fit residues: 56.9997 Evaluate side-chains 263 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 11 optimal weight: 50.0000 chunk 24 optimal weight: 30.0000 chunk 80 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 68 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 63 ASN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.076058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.054802 restraints weight = 85285.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.055907 restraints weight = 46312.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056728 restraints weight = 31722.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.057257 restraints weight = 25292.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057568 restraints weight = 21870.836| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15895 Z= 0.190 Angle : 0.717 8.064 22928 Z= 0.419 Chirality : 0.046 0.272 2563 Planarity : 0.006 0.094 1719 Dihedral : 30.617 162.516 4918 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.58 % Rotamer: Outliers : 0.12 % Allowed : 2.75 % Favored : 97.13 % 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: 1.27 (0.27), residues: 964 helix: 1.59 (0.20), residues: 628 sheet: -1.56 (0.99), residues: 24 loop : -0.41 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.026 0.002 TYR C 50 PHE 0.021 0.002 PHE F 61 TRP 0.021 0.002 TRP P 244 HIS 0.007 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.19 (15895) covalent geometry : angle 0.71685 / 0.42 (22928) hydrogen bonds : bond 0.05644 / 3.64 ( 895) hydrogen bonds : angle 3.57872 / 3.11 ( 2235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.4051 (tpt) cc_final: 0.3270 (mmt) REVERT: P 245 THR cc_start: 0.5949 (OUTLIER) cc_final: 0.5684 (p) REVERT: G 84 GLN cc_start: 0.8937 (tp40) cc_final: 0.8612 (tp-100) REVERT: G 87 ILE cc_start: 0.9585 (mt) cc_final: 0.9330 (mt) REVERT: G 88 ARG cc_start: 0.8774 (mmt180) cc_final: 0.7578 (mtp180) REVERT: G 100 VAL cc_start: 0.9328 (p) cc_final: 0.8960 (p) REVERT: A 51 ILE cc_start: 0.8369 (mt) cc_final: 0.8008 (mt) REVERT: A 61 LEU cc_start: 0.8645 (mt) cc_final: 0.7723 (mt) REVERT: A 87 SER cc_start: 0.9110 (p) cc_final: 0.8468 (t) REVERT: A 105 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8412 (tm-30) REVERT: A 130 ILE cc_start: 0.9432 (mm) cc_final: 0.9212 (mm) REVERT: B 31 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9104 (tmtt) REVERT: B 39 ARG cc_start: 0.9088 (mmt-90) cc_final: 0.8686 (tpp-160) REVERT: B 49 LEU cc_start: 0.9480 (mm) cc_final: 0.9002 (tp) REVERT: B 84 MET cc_start: 0.9321 (mpp) cc_final: 0.9063 (mpp) REVERT: C 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8383 (t0) REVERT: C 92 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8715 (mt-10) REVERT: C 94 ASN cc_start: 0.9459 (t0) cc_final: 0.9241 (m-40) REVERT: D 62 MET cc_start: 0.9076 (mmm) cc_final: 0.8723 (mmm) REVERT: D 85 LYS cc_start: 0.9485 (mtpt) cc_final: 0.9053 (mmmt) REVERT: E 50 GLU cc_start: 0.9056 (tp30) cc_final: 0.8737 (tp30) REVERT: E 60 LEU cc_start: 0.9030 (mm) cc_final: 0.8700 (mm) REVERT: E 74 ILE cc_start: 0.9443 (mt) cc_final: 0.9127 (mt) REVERT: E 77 ASP cc_start: 0.9503 (m-30) cc_final: 0.9259 (m-30) REVERT: E 90 MET cc_start: 0.9423 (mmp) cc_final: 0.9219 (mmp) REVERT: E 93 GLN cc_start: 0.8986 (tt0) cc_final: 0.8525 (tt0) REVERT: E 120 MET cc_start: 0.9042 (mmm) cc_final: 0.8425 (mmm) REVERT: F 63 GLU cc_start: 0.9286 (pt0) cc_final: 0.8809 (pp20) REVERT: F 64 ASN cc_start: 0.9030 (m-40) cc_final: 0.7709 (m-40) REVERT: F 84 MET cc_start: 0.9094 (tpt) cc_final: 0.8726 (tpp) REVERT: F 87 VAL cc_start: 0.9714 (t) cc_final: 0.9442 (t) REVERT: F 91 LYS cc_start: 0.9602 (tttt) cc_final: 0.9218 (ptpt) REVERT: H 46 LYS cc_start: 0.9496 (ptpp) cc_final: 0.8726 (ptpp) REVERT: H 47 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 49 HIS cc_start: 0.8915 (m-70) cc_final: 0.8591 (m90) REVERT: H 59 MET cc_start: 0.8955 (tpp) cc_final: 0.8627 (tpp) REVERT: H 109 HIS cc_start: 0.8676 (m-70) cc_final: 0.8109 (m-70) REVERT: H 113 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8665 (mm-30) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1285 time to fit residues: 56.3824 Evaluate side-chains 258 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056001 restraints weight = 82371.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057166 restraints weight = 43993.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.057969 restraints weight = 29567.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.058487 restraints weight = 23376.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.058811 restraints weight = 20067.022| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15895 Z= 0.158 Angle : 0.698 10.261 22928 Z= 0.407 Chirality : 0.046 0.308 2563 Planarity : 0.006 0.095 1719 Dihedral : 30.687 161.876 4918 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.80 % Favored : 96.99 % Rotamer: Outliers : 0.12 % Allowed : 1.44 % Favored : 98.44 % 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: 1.29 (0.27), residues: 964 helix: 1.58 (0.20), residues: 628 sheet: -1.51 (1.01), residues: 24 loop : -0.37 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 31 TYR 0.023 0.002 TYR C 50 PHE 0.021 0.002 PHE F 61 TRP 0.023 0.002 TRP P 244 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (15895) covalent geometry : angle 0.69788 / 0.41 (22928) hydrogen bonds : bond 0.04756 / 3.07 ( 895) hydrogen bonds : angle 3.41920 / 2.96 ( 2235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.4261 (tpt) cc_final: 0.3535 (mmt) REVERT: G 68 ASN cc_start: 0.9631 (m-40) cc_final: 0.9407 (m110) REVERT: G 84 GLN cc_start: 0.8903 (tp40) cc_final: 0.8695 (tp40) REVERT: G 88 ARG cc_start: 0.8686 (mmt180) cc_final: 0.7642 (mtp180) REVERT: G 100 VAL cc_start: 0.9320 (p) cc_final: 0.8965 (p) REVERT: A 50 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9105 (tt0) REVERT: A 61 LEU cc_start: 0.8494 (mt) cc_final: 0.7560 (mt) REVERT: A 87 SER cc_start: 0.9095 (p) cc_final: 0.8463 (t) REVERT: A 105 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8383 (tm-30) REVERT: A 130 ILE cc_start: 0.9441 (mm) cc_final: 0.9202 (mm) REVERT: B 49 LEU cc_start: 0.9415 (mm) cc_final: 0.8894 (tp) REVERT: B 68 ASP cc_start: 0.8637 (m-30) cc_final: 0.8342 (m-30) REVERT: B 84 MET cc_start: 0.9305 (mpp) cc_final: 0.9025 (mpp) REVERT: C 74 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9115 (mppt) REVERT: C 90 ASP cc_start: 0.8606 (t0) cc_final: 0.8343 (t0) REVERT: C 92 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8660 (mt-10) REVERT: C 94 ASN cc_start: 0.9451 (t0) cc_final: 0.9225 (m-40) REVERT: E 50 GLU cc_start: 0.9036 (tp30) cc_final: 0.8715 (tp30) REVERT: E 60 LEU cc_start: 0.9172 (mm) cc_final: 0.8797 (mm) REVERT: E 73 GLU cc_start: 0.9205 (pt0) cc_final: 0.8731 (pt0) REVERT: E 74 ILE cc_start: 0.9442 (mt) cc_final: 0.9136 (mt) REVERT: E 77 ASP cc_start: 0.9489 (m-30) cc_final: 0.9238 (m-30) REVERT: E 90 MET cc_start: 0.9440 (mmp) cc_final: 0.9235 (mmp) REVERT: E 93 GLN cc_start: 0.8693 (tt0) cc_final: 0.8400 (tt0) REVERT: E 120 MET cc_start: 0.9079 (mmm) cc_final: 0.8509 (mmm) REVERT: F 63 GLU cc_start: 0.9300 (pt0) cc_final: 0.8897 (pp20) REVERT: F 84 MET cc_start: 0.9071 (tpt) cc_final: 0.8630 (tpp) REVERT: F 87 VAL cc_start: 0.9695 (t) cc_final: 0.9495 (t) REVERT: F 91 LYS cc_start: 0.9644 (tttt) cc_final: 0.9260 (ptpt) REVERT: H 47 GLN cc_start: 0.9173 (tm-30) cc_final: 0.8899 (tm-30) REVERT: H 49 HIS cc_start: 0.8897 (m-70) cc_final: 0.8598 (m90) REVERT: H 68 ASP cc_start: 0.8768 (t0) cc_final: 0.8561 (t0) REVERT: H 69 ILE cc_start: 0.8926 (mm) cc_final: 0.8569 (mm) REVERT: H 113 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8619 (mm-30) REVERT: H 116 LYS cc_start: 0.9262 (pttm) cc_final: 0.9060 (pttm) outliers start: 1 outliers final: 1 residues processed: 309 average time/residue: 0.1334 time to fit residues: 59.2239 Evaluate side-chains 263 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 82 HIS H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.073364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052365 restraints weight = 88351.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053447 restraints weight = 47728.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.054204 restraints weight = 32819.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.054672 restraints weight = 26185.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054849 restraints weight = 23067.332| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15895 Z= 0.252 Angle : 0.788 8.355 22928 Z= 0.451 Chirality : 0.047 0.248 2563 Planarity : 0.007 0.098 1719 Dihedral : 30.819 160.418 4918 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.16 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % 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: 0.88 (0.27), residues: 964 helix: 1.25 (0.20), residues: 628 sheet: -1.97 (0.95), residues: 24 loop : -0.46 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 52 TYR 0.035 0.003 TYR B 88 PHE 0.027 0.002 PHE F 61 TRP 0.022 0.003 TRP P 244 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.25 (15895) covalent geometry : angle 0.78806 / 0.45 (22928) hydrogen bonds : bond 0.07415 / 4.78 ( 895) hydrogen bonds : angle 3.90971 / 3.40 ( 2235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7916 (mtm) cc_final: 0.7640 (mpp) REVERT: P 181 MET cc_start: 0.4026 (tpt) cc_final: 0.3347 (mmt) REVERT: G 88 ARG cc_start: 0.8647 (mmt180) cc_final: 0.7634 (mtp180) REVERT: G 100 VAL cc_start: 0.9358 (p) cc_final: 0.9002 (p) REVERT: A 61 LEU cc_start: 0.8319 (mt) cc_final: 0.8092 (mt) REVERT: A 87 SER cc_start: 0.9166 (p) cc_final: 0.8563 (t) REVERT: A 105 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8327 (tm-30) REVERT: B 31 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9059 (tmtt) REVERT: B 43 VAL cc_start: 0.9114 (t) cc_final: 0.8717 (p) REVERT: B 68 ASP cc_start: 0.8637 (m-30) cc_final: 0.8393 (m-30) REVERT: B 84 MET cc_start: 0.9339 (mpp) cc_final: 0.9050 (mpp) REVERT: C 74 LYS cc_start: 0.9351 (mmtm) cc_final: 0.9105 (mppt) REVERT: C 90 ASP cc_start: 0.8780 (t0) cc_final: 0.8501 (t0) REVERT: C 92 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8718 (mt-10) REVERT: C 94 ASN cc_start: 0.9478 (t0) cc_final: 0.9275 (m-40) REVERT: D 62 MET cc_start: 0.9141 (mmm) cc_final: 0.8896 (mmm) REVERT: D 85 LYS cc_start: 0.9628 (mtmt) cc_final: 0.9189 (mmmt) REVERT: E 50 GLU cc_start: 0.8974 (tp30) cc_final: 0.8039 (tp30) REVERT: E 60 LEU cc_start: 0.9210 (mm) cc_final: 0.8860 (mm) REVERT: E 74 ILE cc_start: 0.9454 (mt) cc_final: 0.9251 (mt) REVERT: E 77 ASP cc_start: 0.9361 (m-30) cc_final: 0.9129 (m-30) REVERT: E 82 LEU cc_start: 0.8367 (mt) cc_final: 0.8163 (mt) REVERT: E 93 GLN cc_start: 0.9075 (tt0) cc_final: 0.8402 (tt0) REVERT: E 105 GLU cc_start: 0.8771 (pp20) cc_final: 0.8290 (pp20) REVERT: E 120 MET cc_start: 0.9078 (mmm) cc_final: 0.8601 (mmm) REVERT: F 63 GLU cc_start: 0.9209 (pt0) cc_final: 0.8816 (pp20) REVERT: F 84 MET cc_start: 0.9039 (tpt) cc_final: 0.8585 (tpp) REVERT: F 87 VAL cc_start: 0.9768 (t) cc_final: 0.9432 (t) REVERT: F 91 LYS cc_start: 0.9637 (tttt) cc_final: 0.9287 (ptpt) REVERT: H 47 GLN cc_start: 0.9287 (tm-30) cc_final: 0.9031 (tm-30) REVERT: H 49 HIS cc_start: 0.8909 (m-70) cc_final: 0.8638 (m90) REVERT: H 59 MET cc_start: 0.8815 (tpp) cc_final: 0.8263 (tpp) REVERT: H 82 HIS cc_start: 0.9092 (OUTLIER) cc_final: 0.8700 (m90) REVERT: H 109 HIS cc_start: 0.8575 (m90) cc_final: 0.8187 (m90) REVERT: H 113 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8557 (mm-30) outliers start: 1 outliers final: 0 residues processed: 282 average time/residue: 0.1284 time to fit residues: 52.6237 Evaluate side-chains 234 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 75 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 212 GLN ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.076416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.054977 restraints weight = 84771.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056071 restraints weight = 46182.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056848 restraints weight = 31699.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057406 restraints weight = 25204.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.057720 restraints weight = 21915.886| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15895 Z= 0.157 Angle : 0.729 11.591 22928 Z= 0.421 Chirality : 0.047 0.266 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.813 156.489 4918 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 1.09 (0.27), residues: 964 helix: 1.42 (0.20), residues: 628 sheet: -2.04 (0.90), residues: 24 loop : -0.39 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.023 0.002 TYR G 39 PHE 0.019 0.002 PHE B 61 TRP 0.022 0.002 TRP P 244 HIS 0.008 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (15895) covalent geometry : angle 0.72949 / 0.42 (22928) hydrogen bonds : bond 0.04591 / 2.95 ( 895) hydrogen bonds : angle 3.54574 / 3.04 ( 2235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.8041 (mtm) cc_final: 0.7823 (mpp) REVERT: P 181 MET cc_start: 0.4344 (tpt) cc_final: 0.3724 (mmt) REVERT: G 68 ASN cc_start: 0.9595 (m-40) cc_final: 0.9339 (m110) REVERT: G 84 GLN cc_start: 0.8919 (tp40) cc_final: 0.8632 (tp-100) REVERT: G 88 ARG cc_start: 0.8538 (mmt180) cc_final: 0.7544 (mtp180) REVERT: G 100 VAL cc_start: 0.9329 (p) cc_final: 0.8980 (p) REVERT: A 50 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9086 (tt0) REVERT: A 61 LEU cc_start: 0.8539 (mt) cc_final: 0.8137 (mt) REVERT: A 87 SER cc_start: 0.9134 (p) cc_final: 0.8435 (t) REVERT: A 105 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8339 (tm-30) REVERT: A 120 MET cc_start: 0.8659 (mmt) cc_final: 0.8138 (mmm) REVERT: A 130 ILE cc_start: 0.9371 (mm) cc_final: 0.8997 (mm) REVERT: B 31 LYS cc_start: 0.9317 (tmtt) cc_final: 0.9037 (tmtt) REVERT: B 49 LEU cc_start: 0.9437 (mm) cc_final: 0.8911 (tp) REVERT: B 84 MET cc_start: 0.9319 (mpp) cc_final: 0.9065 (mpp) REVERT: C 74 LYS cc_start: 0.9347 (mmtm) cc_final: 0.9105 (mppt) REVERT: C 90 ASP cc_start: 0.8646 (t0) cc_final: 0.8376 (t0) REVERT: E 50 GLU cc_start: 0.8890 (tp30) cc_final: 0.8571 (tp30) REVERT: E 74 ILE cc_start: 0.9460 (mt) cc_final: 0.9152 (mt) REVERT: E 77 ASP cc_start: 0.9347 (m-30) cc_final: 0.9104 (m-30) REVERT: E 82 LEU cc_start: 0.8474 (mt) cc_final: 0.8069 (mt) REVERT: E 93 GLN cc_start: 0.8865 (tt0) cc_final: 0.8517 (tt0) REVERT: E 120 MET cc_start: 0.9093 (mmm) cc_final: 0.8538 (mmm) REVERT: F 63 GLU cc_start: 0.9245 (pt0) cc_final: 0.8873 (pp20) REVERT: F 87 VAL cc_start: 0.9699 (t) cc_final: 0.9470 (t) REVERT: F 88 TYR cc_start: 0.8804 (m-10) cc_final: 0.8308 (m-80) REVERT: F 91 LYS cc_start: 0.9621 (tttt) cc_final: 0.9242 (ptpt) REVERT: H 46 LYS cc_start: 0.9510 (ptpp) cc_final: 0.9179 (mmtt) REVERT: H 47 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8877 (tm-30) REVERT: H 49 HIS cc_start: 0.8780 (m-70) cc_final: 0.8176 (m90) REVERT: H 59 MET cc_start: 0.8927 (tpp) cc_final: 0.8471 (tpp) REVERT: H 113 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8540 (mm-30) REVERT: H 116 LYS cc_start: 0.9186 (pttm) cc_final: 0.8928 (pttm) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1310 time to fit residues: 57.1736 Evaluate side-chains 253 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 46 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.076633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055782 restraints weight = 84325.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.056880 restraints weight = 44941.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057704 restraints weight = 30376.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058269 restraints weight = 24075.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058622 restraints weight = 20658.151| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15895 Z= 0.154 Angle : 0.733 12.171 22928 Z= 0.421 Chirality : 0.046 0.262 2563 Planarity : 0.006 0.095 1719 Dihedral : 30.725 152.219 4918 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.87 (0.27), residues: 964 helix: 1.26 (0.20), residues: 626 sheet: -1.88 (0.96), residues: 24 loop : -0.50 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.021 0.002 TYR G 39 PHE 0.023 0.002 PHE F 61 TRP 0.022 0.002 TRP P 244 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (15895) covalent geometry : angle 0.73277 / 0.42 (22928) hydrogen bonds : bond 0.04631 / 2.96 ( 895) hydrogen bonds : angle 3.49526 / 3.01 ( 2235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.8024 (mtm) cc_final: 0.7803 (mpp) REVERT: P 181 MET cc_start: 0.4286 (tpt) cc_final: 0.3539 (mmt) REVERT: P 207 TYR cc_start: 0.6355 (t80) cc_final: 0.6116 (t80) REVERT: G 68 ASN cc_start: 0.9584 (m-40) cc_final: 0.9377 (m110) REVERT: G 84 GLN cc_start: 0.8902 (tp40) cc_final: 0.8590 (tp-100) REVERT: G 88 ARG cc_start: 0.8520 (mmt180) cc_final: 0.7445 (mtp180) REVERT: G 100 VAL cc_start: 0.9319 (p) cc_final: 0.8861 (p) REVERT: A 50 GLU cc_start: 0.9360 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 51 ILE cc_start: 0.8292 (mt) cc_final: 0.8087 (mt) REVERT: A 87 SER cc_start: 0.9086 (p) cc_final: 0.8452 (t) REVERT: A 94 GLU cc_start: 0.8775 (mm-30) cc_final: 0.7988 (mt-10) REVERT: A 120 MET cc_start: 0.8381 (mmt) cc_final: 0.7656 (mmm) REVERT: A 126 LEU cc_start: 0.9760 (tp) cc_final: 0.9530 (mm) REVERT: B 31 LYS cc_start: 0.9297 (tmtt) cc_final: 0.9005 (tmtt) REVERT: B 39 ARG cc_start: 0.9019 (mmt-90) cc_final: 0.7985 (tpp-160) REVERT: B 49 LEU cc_start: 0.9384 (mm) cc_final: 0.8936 (tp) REVERT: B 68 ASP cc_start: 0.8617 (m-30) cc_final: 0.8353 (m-30) REVERT: B 84 MET cc_start: 0.9358 (mpp) cc_final: 0.9074 (mpp) REVERT: B 96 THR cc_start: 0.8758 (m) cc_final: 0.8331 (p) REVERT: C 74 LYS cc_start: 0.9289 (mmtm) cc_final: 0.9058 (mppt) REVERT: C 79 ILE cc_start: 0.9029 (tt) cc_final: 0.8691 (mm) REVERT: C 90 ASP cc_start: 0.8280 (t0) cc_final: 0.7999 (t0) REVERT: D 83 TYR cc_start: 0.8207 (m-10) cc_final: 0.7976 (m-10) REVERT: E 50 GLU cc_start: 0.8976 (tp30) cc_final: 0.8666 (tp30) REVERT: E 73 GLU cc_start: 0.9186 (pt0) cc_final: 0.8593 (pt0) REVERT: E 74 ILE cc_start: 0.9462 (mt) cc_final: 0.9164 (mt) REVERT: E 77 ASP cc_start: 0.9339 (m-30) cc_final: 0.9113 (m-30) REVERT: E 93 GLN cc_start: 0.8706 (tt0) cc_final: 0.8480 (tt0) REVERT: E 105 GLU cc_start: 0.8761 (pp20) cc_final: 0.8250 (pp20) REVERT: E 106 ASP cc_start: 0.9078 (m-30) cc_final: 0.8798 (m-30) REVERT: E 120 MET cc_start: 0.9107 (mmm) cc_final: 0.8500 (mmm) REVERT: F 25 ASN cc_start: 0.8351 (m-40) cc_final: 0.7759 (m-40) REVERT: F 63 GLU cc_start: 0.9268 (pt0) cc_final: 0.8890 (pp20) REVERT: F 68 ASP cc_start: 0.9021 (m-30) cc_final: 0.8812 (m-30) REVERT: F 84 MET cc_start: 0.8946 (tpt) cc_final: 0.8551 (tpp) REVERT: F 91 LYS cc_start: 0.9596 (tttt) cc_final: 0.9196 (ptpt) REVERT: F 100 PHE cc_start: 0.8454 (m-10) cc_final: 0.8240 (m-10) REVERT: H 34 LYS cc_start: 0.9310 (mmmt) cc_final: 0.9096 (mmmm) REVERT: H 46 LYS cc_start: 0.9501 (ptpp) cc_final: 0.9173 (mmtt) REVERT: H 47 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8912 (tm-30) REVERT: H 49 HIS cc_start: 0.8756 (m-70) cc_final: 0.8090 (m-70) REVERT: H 59 MET cc_start: 0.8812 (tpp) cc_final: 0.8229 (tpp) REVERT: H 87 SER cc_start: 0.9221 (m) cc_final: 0.9011 (m) REVERT: H 113 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8609 (mm-30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1250 time to fit residues: 54.5524 Evaluate side-chains 262 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056405 restraints weight = 82653.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057589 restraints weight = 43778.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058458 restraints weight = 29547.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059060 restraints weight = 23262.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059519 restraints weight = 20095.199| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15895 Z= 0.152 Angle : 0.718 10.936 22928 Z= 0.416 Chirality : 0.045 0.237 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.670 151.232 4918 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 0.88 (0.27), residues: 964 helix: 1.30 (0.20), residues: 626 sheet: -2.10 (0.90), residues: 24 loop : -0.55 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 265 TYR 0.019 0.002 TYR H 42 PHE 0.012 0.001 PHE D 65 TRP 0.016 0.002 TRP P 244 HIS 0.014 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (15895) covalent geometry : angle 0.71788 / 0.42 (22928) hydrogen bonds : bond 0.04475 / 2.87 ( 895) hydrogen bonds : angle 3.47986 / 3.00 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.33 seconds wall clock time: 47 minutes 38.09 seconds (2858.09 seconds total)