Starting phenix.real_space_refine on Fri Jul 3 14:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vfz_43195/07_2026/8vfz_43195.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vfz_43195/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vfz_43195/07_2026/8vfz_43195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vfz_43195/07_2026/8vfz_43195.map" model { file = "/net/cci-nas-00/data/ceres_data/8vfz_43195/07_2026/8vfz_43195.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vfz_43195/07_2026/8vfz_43195.cif" } 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-dev-6108/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: 3.20, per 1000 atoms: 0.21 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: 1.05 Conformation dependent library (CDL) restraints added in 471.8 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: 1.99 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: 2.55 Time building geometry restraints manager: 1.44 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: 20899 1.41 - 2.81: 1642 2.81 - 4.22: 364 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.090 Find NCS groups from input model: 0.150 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: 17.830 ------------------------------------------------------------------------------- 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 : 0.826 7.031 22928 Z= 0.729 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 0.82570 / 0.73 (22928) hydrogen bonds : bond 0.09641 / 6.13 ( 895) hydrogen bonds : angle 3.61872 / 3.04 ( 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 : 0.388 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: O 204 PHE cc_start: 0.9280 (m-80) cc_final: 0.9021 (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: 0.3495 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9049 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8073 (mm-40) REVERT: G 34 LEU cc_start: 0.9644 (mt) cc_final: 0.9436 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8384 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9324 (mt) REVERT: G 84 GLN cc_start: 0.9004 (tp40) cc_final: 0.8797 (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: 0.8999 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.7994 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8643 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8687 (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: 0.8504 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8427 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8498 (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: 0.9590 (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: 0.8305 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.8002 (t80) REVERT: C 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9477 (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: 0.8917 (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: 0.8534 (p) REVERT: D 89 ILE cc_start: 0.9390 (mt) cc_final: 0.9187 (tp) REVERT: E 48 LEU cc_start: 0.9319 (mt) cc_final: 0.8954 (mt) REVERT: E 60 LEU cc_start: 0.9209 (mt) cc_final: 0.7993 (mp) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8248 (tm-30) REVERT: E 109 LEU cc_start: 0.9645 (mt) cc_final: 0.9151 (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: 0.8448 (m110) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8702 (m-30) REVERT: F 84 MET cc_start: 0.9140 (mmm) cc_final: 0.8935 (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: 0.9110 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8656 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8482 (t0) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8212 (p) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8338 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8787 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.1363 time to fit residues: 86.2676 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 : 0.382 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 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: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 215 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.077644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056293 restraints weight = 85349.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057532 restraints weight = 45197.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.058340 restraints weight = 30322.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058964 restraints weight = 23867.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.059262 restraints weight = 20397.899| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15895 Z= 0.212 Angle : 0.750 10.007 22928 Z= 0.443 Chirality : 0.049 0.240 2563 Planarity : 0.007 0.094 1719 Dihedral : 29.980 165.895 4918 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.49 % Favored : 97.20 % Rotamer: Outliers : 0.36 % Allowed : 3.95 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.27), residues: 964 helix: 2.34 (0.20), residues: 626 sheet: -1.62 (1.02), residues: 24 loop : -0.34 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 213 TYR 0.034 0.002 TYR G 39 PHE 0.018 0.002 PHE G 25 TRP 0.022 0.003 TRP P 214 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (15895) covalent geometry : angle 0.74974 / 0.44 (22928) hydrogen bonds : bond 0.06306 / 4.06 ( 895) hydrogen bonds : angle 3.57192 / 3.11 ( 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 343 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 0.360 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: O 204 PHE cc_start: 0.9188 (m-80) cc_final: 0.8980 (m-80) REVERT: O 215 GLN cc_start: 0.9454 (pt0) cc_final: 0.9229 (pt0) REVERT: P 181 MET cc_start: 0.3800 (tpt) cc_final: 0.3063 (mmt) REVERT: G 24 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8072 (mm-40) REVERT: G 58 LEU cc_start: 0.9684 (mm) cc_final: 0.9380 (mm) REVERT: G 64 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.8797 (pp20) REVERT: G 68 ASN cc_start: 0.9614 (m-40) cc_final: 0.8856 (m110) REVERT: G 83 LEU cc_start: 0.9590 (mt) cc_final: 0.9365 (mt) REVERT: G 84 GLN cc_start: 0.9021 (tp40) cc_final: 0.8576 (tp-100) REVERT: G 87 ILE cc_start: 0.9547 (mt) cc_final: 0.9219 (tp) REVERT: G 88 ARG cc_start: 0.8860 (mmt180) cc_final: 0.7888 (mtp180) REVERT: G 100 VAL cc_start: 0.9325 (t) cc_final: 0.9031 (p) REVERT: G 107 VAL cc_start: 0.9008 (m) cc_final: 0.8672 (p) REVERT: A 50 GLU cc_start: 0.9439 (mt-10) cc_final: 0.8868 (mt-10) REVERT: A 51 ILE cc_start: 0.8384 (mt) cc_final: 0.8059 (mt) REVERT: A 53 ARG cc_start: 0.9653 (ptm-80) cc_final: 0.9439 (ptm160) REVERT: A 61 LEU cc_start: 0.8624 (mt) cc_final: 0.8392 (mt) REVERT: A 87 SER cc_start: 0.8972 (p) cc_final: 0.8397 (t) REVERT: A 90 MET cc_start: 0.8866 (mpp) cc_final: 0.8518 (mmm) REVERT: A 105 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8485 (tm-30) REVERT: A 126 LEU cc_start: 0.9535 (mm) cc_final: 0.9123 (mm) REVERT: A 130 ILE cc_start: 0.9581 (mm) cc_final: 0.9322 (mm) REVERT: B 25 ASN cc_start: 0.7919 (m110) cc_final: 0.4931 (m110) REVERT: B 31 LYS cc_start: 0.9545 (tmtt) cc_final: 0.9337 (tmmt) REVERT: B 39 ARG cc_start: 0.9249 (mmt-90) cc_final: 0.8675 (tpp-160) REVERT: B 49 LEU cc_start: 0.9511 (mm) cc_final: 0.9019 (tp) REVERT: B 63 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8482 (mp0) REVERT: B 64 ASN cc_start: 0.8980 (m-40) cc_final: 0.8719 (t0) REVERT: B 78 ARG cc_start: 0.8572 (mtm110) cc_final: 0.7956 (mtm110) REVERT: B 84 MET cc_start: 0.9334 (mpp) cc_final: 0.9068 (mpp) REVERT: C 50 TYR cc_start: 0.8421 (t80) cc_final: 0.7890 (t80) REVERT: C 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8408 (t0) REVERT: D 62 MET cc_start: 0.9136 (mmm) cc_final: 0.8584 (mmm) REVERT: D 76 GLU cc_start: 0.9401 (tp30) cc_final: 0.9184 (tp30) REVERT: D 85 LYS cc_start: 0.9383 (mtpt) cc_final: 0.9077 (mmmt) REVERT: D 89 ILE cc_start: 0.9505 (mt) cc_final: 0.9204 (tp) REVERT: E 120 MET cc_start: 0.8818 (mmm) cc_final: 0.8536 (mmm) REVERT: E 126 LEU cc_start: 0.9182 (tp) cc_final: 0.8912 (tt) REVERT: F 44 LYS cc_start: 0.9024 (tptm) cc_final: 0.8390 (tptm) REVERT: F 64 ASN cc_start: 0.8939 (m-40) cc_final: 0.8474 (m110) REVERT: H 52 THR cc_start: 0.8505 (t) cc_final: 0.8256 (t) REVERT: H 59 MET cc_start: 0.8994 (tpp) cc_final: 0.8558 (tpp) REVERT: H 69 ILE cc_start: 0.9057 (mm) cc_final: 0.8785 (mm) REVERT: H 113 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8976 (mm-30) outliers start: 3 outliers final: 1 residues processed: 342 average time/residue: 0.1261 time to fit residues: 61.4780 Evaluate side-chains 264 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 8.9990 chunk 41 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 210 ASN ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054628 restraints weight = 86695.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.055886 restraints weight = 45765.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056649 restraints weight = 30707.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057254 restraints weight = 24200.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057539 restraints weight = 20869.873| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15895 Z= 0.206 Angle : 0.715 8.481 22928 Z= 0.426 Chirality : 0.046 0.264 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.366 165.624 4918 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.28 % Favored : 97.41 % Rotamer: Outliers : 0.48 % Allowed : 4.19 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.67 (0.27), residues: 964 helix: 2.00 (0.20), residues: 628 sheet: -1.49 (1.06), residues: 24 loop : -0.49 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 83 TYR 0.020 0.002 TYR G 39 PHE 0.023 0.002 PHE E 78 TRP 0.021 0.003 TRP P 214 HIS 0.005 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 (15895) covalent geometry : angle 0.71464 / 0.43 (22928) hydrogen bonds : bond 0.05828 / 3.75 ( 895) hydrogen bonds : angle 3.57521 / 3.16 ( 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 318 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 0.460 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: P 181 MET cc_start: 0.3820 (tpt) cc_final: 0.3084 (mmt) REVERT: P 201 MET cc_start: 0.0426 (mmt) cc_final: 0.0209 (mmt) REVERT: G 25 PHE cc_start: 0.8463 (m-10) cc_final: 0.8193 (m-10) REVERT: G 38 ASN cc_start: 0.9129 (t0) cc_final: 0.8776 (t0) REVERT: G 58 LEU cc_start: 0.9666 (mm) cc_final: 0.9339 (mm) REVERT: G 64 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8857 (pp20) REVERT: G 68 ASN cc_start: 0.9671 (m-40) cc_final: 0.9149 (m110) REVERT: G 84 GLN cc_start: 0.8975 (tp40) cc_final: 0.8759 (tp-100) REVERT: G 88 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8161 (mtp180) REVERT: G 92 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8051 (tt0) REVERT: G 100 VAL cc_start: 0.9356 (t) cc_final: 0.8863 (p) REVERT: A 51 ILE cc_start: 0.8358 (mt) cc_final: 0.8130 (mt) REVERT: A 53 ARG cc_start: 0.9655 (ptm-80) cc_final: 0.9245 (ptm160) REVERT: A 54 TYR cc_start: 0.9563 (m-80) cc_final: 0.8804 (m-80) REVERT: A 61 LEU cc_start: 0.8915 (mt) cc_final: 0.8233 (mt) REVERT: A 87 SER cc_start: 0.9030 (p) cc_final: 0.8281 (t) REVERT: A 90 MET cc_start: 0.8966 (mpp) cc_final: 0.8693 (mpp) REVERT: A 105 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8520 (tm-30) REVERT: A 130 ILE cc_start: 0.9554 (mm) cc_final: 0.9300 (mm) REVERT: B 39 ARG cc_start: 0.9283 (mmt-90) cc_final: 0.9046 (tpp-160) REVERT: B 49 LEU cc_start: 0.9515 (mm) cc_final: 0.9018 (tp) REVERT: B 63 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8580 (mp0) REVERT: B 64 ASN cc_start: 0.8963 (m-40) cc_final: 0.8713 (t0) REVERT: B 66 ILE cc_start: 0.9809 (mm) cc_final: 0.9564 (pt) REVERT: B 78 ARG cc_start: 0.8965 (mtm110) cc_final: 0.8158 (mtm110) REVERT: B 84 MET cc_start: 0.9378 (mpp) cc_final: 0.9081 (mpp) REVERT: C 78 ILE cc_start: 0.8540 (mm) cc_final: 0.8254 (tp) REVERT: C 87 ILE cc_start: 0.9332 (mt) cc_final: 0.9107 (mt) REVERT: C 90 ASP cc_start: 0.8614 (t0) cc_final: 0.8361 (t0) REVERT: C 92 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8613 (mm-30) REVERT: C 94 ASN cc_start: 0.9483 (t0) cc_final: 0.9246 (m-40) REVERT: D 62 MET cc_start: 0.9212 (mmm) cc_final: 0.8892 (mmm) REVERT: D 85 LYS cc_start: 0.9420 (mtpt) cc_final: 0.9121 (mmmt) REVERT: E 50 GLU cc_start: 0.9168 (tp30) cc_final: 0.8210 (tp30) REVERT: E 60 LEU cc_start: 0.9160 (mm) cc_final: 0.8727 (mm) REVERT: E 74 ILE cc_start: 0.9354 (mt) cc_final: 0.9062 (mt) REVERT: E 77 ASP cc_start: 0.9592 (m-30) cc_final: 0.9376 (m-30) REVERT: E 81 ASP cc_start: 0.8856 (m-30) cc_final: 0.8647 (m-30) REVERT: E 120 MET cc_start: 0.8875 (mmm) cc_final: 0.8551 (mmm) REVERT: E 126 LEU cc_start: 0.9193 (tp) cc_final: 0.8991 (tp) REVERT: F 64 ASN cc_start: 0.8866 (m-40) cc_final: 0.8499 (m110) REVERT: F 84 MET cc_start: 0.9283 (tpt) cc_final: 0.8827 (tpp) REVERT: F 87 VAL cc_start: 0.9705 (t) cc_final: 0.9467 (t) REVERT: F 91 LYS cc_start: 0.9472 (ttpt) cc_final: 0.9133 (ptpt) REVERT: H 49 HIS cc_start: 0.8987 (m-70) cc_final: 0.8601 (m90) REVERT: H 59 MET cc_start: 0.9128 (tpp) cc_final: 0.8760 (tpp) REVERT: H 69 ILE cc_start: 0.9061 (mm) cc_final: 0.8746 (mm) REVERT: H 86 ARG cc_start: 0.9065 (mmt-90) cc_final: 0.8842 (tpp-160) REVERT: H 105 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8764 (mm-30) REVERT: H 109 HIS cc_start: 0.8775 (m-70) cc_final: 0.8287 (m-70) REVERT: H 113 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9010 (mm-30) outliers start: 4 outliers final: 0 residues processed: 316 average time/residue: 0.1194 time to fit residues: 54.2693 Evaluate side-chains 267 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 1.9990 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 43 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 225 ASN G 24 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** 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** F 93 GLN H 63 ASN H 82 HIS H 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.053752 restraints weight = 86453.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054964 restraints weight = 45768.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055743 restraints weight = 30703.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056278 restraints weight = 24508.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056611 restraints weight = 21151.147| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15895 Z= 0.223 Angle : 0.721 8.348 22928 Z= 0.426 Chirality : 0.046 0.255 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.579 165.804 4918 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.80 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 3.35 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.54 (0.27), residues: 964 helix: 1.85 (0.20), residues: 628 sheet: -1.19 (1.11), residues: 24 loop : -0.47 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.020 0.002 TYR C 50 PHE 0.020 0.002 PHE F 61 TRP 0.015 0.003 TRP O 214 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.22 (15895) covalent geometry : angle 0.72123 / 0.43 (22928) hydrogen bonds : bond 0.06301 / 4.06 ( 895) hydrogen bonds : angle 3.68569 / 3.22 ( 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 302 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 0.390 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: O 201 MET cc_start: 0.8038 (mtm) cc_final: 0.7801 (mpp) REVERT: P 181 MET cc_start: 0.3838 (tpt) cc_final: 0.3096 (mmt) REVERT: G 58 LEU cc_start: 0.9640 (mm) cc_final: 0.9318 (mm) REVERT: G 84 GLN cc_start: 0.8954 (tp40) cc_final: 0.8611 (tp-100) REVERT: G 88 ARG cc_start: 0.8790 (mmt180) cc_final: 0.7995 (mtp180) REVERT: A 51 ILE cc_start: 0.8389 (mt) cc_final: 0.8050 (mt) REVERT: A 53 ARG cc_start: 0.9654 (ptm-80) cc_final: 0.9334 (ptm160) REVERT: A 61 LEU cc_start: 0.8765 (mt) cc_final: 0.7936 (mt) REVERT: A 87 SER cc_start: 0.9085 (p) cc_final: 0.8542 (t) REVERT: A 90 MET cc_start: 0.8909 (mpp) cc_final: 0.8573 (mmm) REVERT: A 105 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8406 (tm-30) REVERT: A 130 ILE cc_start: 0.9598 (mm) cc_final: 0.9369 (mm) REVERT: B 39 ARG cc_start: 0.9148 (mmt-90) cc_final: 0.8843 (tpp-160) REVERT: B 49 LEU cc_start: 0.9492 (mm) cc_final: 0.8996 (tp) REVERT: B 84 MET cc_start: 0.9337 (mpp) cc_final: 0.9063 (mpp) REVERT: C 78 ILE cc_start: 0.8574 (mm) cc_final: 0.8345 (tp) REVERT: C 90 ASP cc_start: 0.8799 (t0) cc_final: 0.8589 (t0) REVERT: C 92 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8750 (mt-10) REVERT: D 62 MET cc_start: 0.9275 (mmm) cc_final: 0.8882 (mmm) REVERT: D 68 ASP cc_start: 0.9380 (t0) cc_final: 0.9116 (t0) REVERT: D 76 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8941 (mm-30) REVERT: D 101 LEU cc_start: 0.9122 (tt) cc_final: 0.8887 (tt) REVERT: E 50 GLU cc_start: 0.9164 (tp30) cc_final: 0.8156 (tp30) REVERT: E 60 LEU cc_start: 0.9158 (mm) cc_final: 0.8775 (mm) REVERT: E 74 ILE cc_start: 0.9355 (mt) cc_final: 0.9044 (mt) REVERT: E 77 ASP cc_start: 0.9575 (m-30) cc_final: 0.9374 (m-30) REVERT: E 79 LYS cc_start: 0.8633 (pptt) cc_final: 0.8068 (pptt) REVERT: E 82 LEU cc_start: 0.8110 (mt) cc_final: 0.7271 (mt) REVERT: E 93 GLN cc_start: 0.9162 (tt0) cc_final: 0.8658 (tt0) REVERT: E 120 MET cc_start: 0.9000 (mmm) cc_final: 0.8351 (mmm) REVERT: E 126 LEU cc_start: 0.9265 (tp) cc_final: 0.9054 (tp) REVERT: F 25 ASN cc_start: 0.8584 (m-40) cc_final: 0.8120 (m-40) REVERT: F 49 LEU cc_start: 0.9475 (mm) cc_final: 0.8897 (mt) REVERT: F 63 GLU cc_start: 0.9309 (pt0) cc_final: 0.9065 (pt0) REVERT: F 87 VAL cc_start: 0.9732 (t) cc_final: 0.9463 (t) REVERT: F 88 TYR cc_start: 0.8816 (m-10) cc_final: 0.8551 (m-10) REVERT: F 91 LYS cc_start: 0.9433 (ttpt) cc_final: 0.9190 (ptpt) REVERT: H 42 TYR cc_start: 0.7804 (t80) cc_final: 0.7354 (t80) REVERT: H 49 HIS cc_start: 0.9001 (m-70) cc_final: 0.8528 (m-70) REVERT: H 59 MET cc_start: 0.9040 (tpp) cc_final: 0.8606 (tpp) REVERT: H 69 ILE cc_start: 0.9063 (mm) cc_final: 0.8622 (mm) REVERT: H 82 HIS cc_start: 0.9065 (OUTLIER) cc_final: 0.8761 (m90) REVERT: H 105 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8704 (mm-30) REVERT: H 109 HIS cc_start: 0.8336 (m90) cc_final: 0.8026 (m90) REVERT: H 113 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8579 (mm-30) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.1198 time to fit residues: 51.5743 Evaluate side-chains 255 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 111 optimal weight: 0.0050 chunk 28 optimal weight: 20.0000 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.076371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055486 restraints weight = 85255.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056595 restraints weight = 45297.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057358 restraints weight = 30650.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.057935 restraints weight = 24376.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058199 restraints weight = 21055.492| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15895 Z= 0.172 Angle : 0.698 7.815 22928 Z= 0.414 Chirality : 0.046 0.285 2563 Planarity : 0.006 0.092 1719 Dihedral : 30.686 165.197 4918 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.42 (0.27), residues: 964 helix: 1.71 (0.20), residues: 628 sheet: -1.06 (1.17), residues: 24 loop : -0.40 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.028 0.002 TYR C 50 PHE 0.020 0.002 PHE F 61 TRP 0.014 0.002 TRP O 214 HIS 0.008 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.17 (15895) covalent geometry : angle 0.69815 / 0.41 (22928) hydrogen bonds : bond 0.05132 / 3.27 ( 895) hydrogen bonds : angle 3.49295 / 2.98 ( 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 304 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.467 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: P 181 MET cc_start: 0.3880 (tpt) cc_final: 0.3217 (mmp) REVERT: G 84 GLN cc_start: 0.8944 (tp40) cc_final: 0.8634 (tp-100) REVERT: G 88 ARG cc_start: 0.8762 (mmt180) cc_final: 0.7606 (mtp180) REVERT: G 100 VAL cc_start: 0.9335 (p) cc_final: 0.8939 (p) REVERT: A 53 ARG cc_start: 0.9617 (ptm-80) cc_final: 0.9335 (ptm160) REVERT: A 61 LEU cc_start: 0.8677 (mt) cc_final: 0.7802 (mt) REVERT: A 87 SER cc_start: 0.9138 (p) cc_final: 0.8611 (t) REVERT: A 90 MET cc_start: 0.8895 (mpp) cc_final: 0.8529 (mmm) REVERT: A 105 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8449 (tm-30) REVERT: A 130 ILE cc_start: 0.9467 (mm) cc_final: 0.9196 (mm) REVERT: B 49 LEU cc_start: 0.9475 (mm) cc_final: 0.9016 (tp) REVERT: B 52 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8531 (mp0) REVERT: B 63 GLU cc_start: 0.8363 (pp20) cc_final: 0.7951 (pp20) REVERT: B 84 MET cc_start: 0.9326 (mpp) cc_final: 0.9027 (mpp) REVERT: C 90 ASP cc_start: 0.8740 (t0) cc_final: 0.8449 (t0) REVERT: C 92 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8715 (mt-10) REVERT: C 94 ASN cc_start: 0.9461 (t0) cc_final: 0.9237 (m-40) REVERT: D 62 MET cc_start: 0.9148 (mmm) cc_final: 0.8811 (mmm) REVERT: D 76 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8784 (mm-30) REVERT: E 50 GLU cc_start: 0.9048 (tp30) cc_final: 0.8764 (tp30) REVERT: E 60 LEU cc_start: 0.9195 (mm) cc_final: 0.8772 (mm) REVERT: E 73 GLU cc_start: 0.9392 (pt0) cc_final: 0.8683 (pt0) REVERT: E 74 ILE cc_start: 0.9428 (mt) cc_final: 0.9164 (mt) REVERT: E 82 LEU cc_start: 0.8326 (mt) cc_final: 0.7765 (mt) REVERT: E 93 GLN cc_start: 0.8908 (tt0) cc_final: 0.8515 (tt0) REVERT: E 120 MET cc_start: 0.8989 (mmm) cc_final: 0.8549 (mmm) REVERT: F 25 ASN cc_start: 0.9237 (m-40) cc_final: 0.8390 (m-40) REVERT: F 63 GLU cc_start: 0.9279 (pt0) cc_final: 0.8823 (pp20) REVERT: F 64 ASN cc_start: 0.8931 (m-40) cc_final: 0.7600 (m-40) REVERT: F 84 MET cc_start: 0.9076 (tpt) cc_final: 0.8655 (tpp) REVERT: F 87 VAL cc_start: 0.9730 (t) cc_final: 0.9408 (t) REVERT: H 47 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8807 (tm-30) REVERT: H 49 HIS cc_start: 0.8946 (m-70) cc_final: 0.8606 (m90) REVERT: H 59 MET cc_start: 0.8858 (tpp) cc_final: 0.8600 (tpp) REVERT: H 69 ILE cc_start: 0.8963 (mm) cc_final: 0.8554 (mm) REVERT: H 109 HIS cc_start: 0.8275 (m90) cc_final: 0.7910 (m90) REVERT: H 113 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8714 (mm-30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1214 time to fit residues: 53.9843 Evaluate side-chains 263 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 0.7980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 50.0000 chunk 24 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3641 r_free = 0.3641 target = 0.076420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055429 restraints weight = 85516.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056468 restraints weight = 45680.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057227 restraints weight = 31118.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057698 restraints weight = 24861.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058050 restraints weight = 21951.923| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15895 Z= 0.165 Angle : 0.694 8.014 22928 Z= 0.409 Chirality : 0.045 0.272 2563 Planarity : 0.005 0.093 1719 Dihedral : 30.713 164.514 4918 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.12 % Allowed : 1.56 % Favored : 98.32 % 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: 1.38 (0.27), residues: 964 helix: 1.69 (0.20), residues: 628 sheet: -1.09 (1.09), residues: 24 loop : -0.45 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 88 TYR 0.024 0.002 TYR H 40 PHE 0.020 0.001 PHE F 61 TRP 0.014 0.002 TRP O 214 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (15895) covalent geometry : angle 0.69372 / 0.41 (22928) hydrogen bonds : bond 0.05017 / 3.20 ( 895) hydrogen bonds : angle 3.46758 / 2.96 ( 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 299 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 298 time to evaluate : 0.390 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: O 193 LEU cc_start: 0.9158 (tp) cc_final: 0.8339 (tp) REVERT: P 181 MET cc_start: 0.3657 (tpt) cc_final: 0.3070 (mmp) REVERT: G 64 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8642 (pp20) REVERT: G 68 ASN cc_start: 0.9606 (m-40) cc_final: 0.8900 (m-40) REVERT: G 84 GLN cc_start: 0.8945 (tp40) cc_final: 0.8662 (tp40) REVERT: G 87 ILE cc_start: 0.9452 (mt) cc_final: 0.9199 (tp) REVERT: G 88 ARG cc_start: 0.8711 (mmt180) cc_final: 0.7727 (mtp180) REVERT: G 100 VAL cc_start: 0.9414 (p) cc_final: 0.9080 (p) REVERT: A 53 ARG cc_start: 0.9601 (ptm-80) cc_final: 0.9372 (ptm160) REVERT: A 61 LEU cc_start: 0.8534 (mt) cc_final: 0.7873 (mt) REVERT: A 87 SER cc_start: 0.9111 (p) cc_final: 0.8484 (t) REVERT: A 105 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8420 (tm-30) REVERT: A 120 MET cc_start: 0.8625 (mmt) cc_final: 0.8051 (mmm) REVERT: A 130 ILE cc_start: 0.9452 (mm) cc_final: 0.9229 (mm) REVERT: B 31 LYS cc_start: 0.9508 (tmtt) cc_final: 0.9266 (tmtt) REVERT: B 49 LEU cc_start: 0.9485 (mm) cc_final: 0.9009 (tp) REVERT: B 52 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8549 (mp0) REVERT: B 84 MET cc_start: 0.9305 (mpp) cc_final: 0.8996 (mpp) REVERT: C 74 LYS cc_start: 0.9353 (mmtm) cc_final: 0.9120 (mppt) REVERT: C 90 ASP cc_start: 0.8643 (t0) cc_final: 0.8398 (t0) REVERT: C 92 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8754 (mt-10) REVERT: C 94 ASN cc_start: 0.9456 (t0) cc_final: 0.9239 (m-40) REVERT: D 41 VAL cc_start: 0.9507 (m) cc_final: 0.9268 (p) REVERT: D 62 MET cc_start: 0.9104 (mmm) cc_final: 0.8813 (mmm) REVERT: D 76 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8771 (mm-30) REVERT: E 50 GLU cc_start: 0.9018 (tp30) cc_final: 0.8709 (tp30) REVERT: E 60 LEU cc_start: 0.9098 (mm) cc_final: 0.8752 (mm) REVERT: E 73 GLU cc_start: 0.9317 (pt0) cc_final: 0.8680 (pt0) REVERT: E 74 ILE cc_start: 0.9443 (mt) cc_final: 0.9226 (mt) REVERT: E 82 LEU cc_start: 0.8399 (mt) cc_final: 0.7917 (mt) REVERT: E 93 GLN cc_start: 0.8885 (tt0) cc_final: 0.8646 (tt0) REVERT: E 120 MET cc_start: 0.9118 (mmm) cc_final: 0.8387 (mmm) REVERT: F 25 ASN cc_start: 0.9191 (m-40) cc_final: 0.8282 (m-40) REVERT: F 49 LEU cc_start: 0.9583 (mt) cc_final: 0.9205 (mt) REVERT: F 63 GLU cc_start: 0.9274 (pt0) cc_final: 0.8792 (pp20) REVERT: F 64 ASN cc_start: 0.9039 (m-40) cc_final: 0.7653 (m-40) REVERT: F 84 MET cc_start: 0.9109 (tpt) cc_final: 0.8733 (tpp) REVERT: H 42 TYR cc_start: 0.7544 (t80) cc_final: 0.7131 (t80) REVERT: H 47 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8799 (tm-30) REVERT: H 49 HIS cc_start: 0.8941 (m-70) cc_final: 0.8624 (m90) REVERT: H 59 MET cc_start: 0.8807 (tpp) cc_final: 0.8491 (tpp) REVERT: H 69 ILE cc_start: 0.8940 (mm) cc_final: 0.8543 (mm) REVERT: H 109 HIS cc_start: 0.8365 (m90) cc_final: 0.7960 (m90) REVERT: H 113 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8566 (mm-30) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.1094 time to fit residues: 47.5362 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 : 0.377 ------------------------------------------------------------------------------- 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: 0.7980 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054255 restraints weight = 83720.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055394 restraints weight = 45060.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.056142 restraints weight = 30277.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056647 restraints weight = 23914.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.056997 restraints weight = 20652.780| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15895 Z= 0.212 Angle : 0.731 8.022 22928 Z= 0.427 Chirality : 0.046 0.247 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.788 164.098 4918 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.42 % Favored : 96.37 % Rotamer: Outliers : 0.12 % Allowed : 2.28 % Favored : 97.60 % 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: 1.21 (0.27), residues: 964 helix: 1.53 (0.20), residues: 628 sheet: -1.06 (1.11), residues: 24 loop : -0.47 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.031 0.002 TYR O 197 PHE 0.022 0.002 PHE F 61 TRP 0.016 0.002 TRP O 214 HIS 0.014 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 (15895) covalent geometry : angle 0.73107 / 0.43 (22928) hydrogen bonds : bond 0.06178 / 3.97 ( 895) hydrogen bonds : angle 3.71036 / 3.18 ( 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 291 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.393 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: O 193 LEU cc_start: 0.9251 (tp) cc_final: 0.8571 (tp) REVERT: O 197 TYR cc_start: 0.8654 (m-80) cc_final: 0.8168 (m-80) REVERT: O 201 MET cc_start: 0.7860 (mtm) cc_final: 0.7576 (mpp) REVERT: P 181 MET cc_start: 0.3816 (tpt) cc_final: 0.3116 (mmp) REVERT: G 84 GLN cc_start: 0.8970 (tp40) cc_final: 0.8712 (tp-100) REVERT: G 88 ARG cc_start: 0.8715 (mmt180) cc_final: 0.7566 (mtp180) REVERT: G 100 VAL cc_start: 0.9398 (p) cc_final: 0.9038 (p) REVERT: A 53 ARG cc_start: 0.9615 (ptm-80) cc_final: 0.9379 (ptm160) REVERT: A 87 SER cc_start: 0.9146 (p) cc_final: 0.8529 (t) REVERT: A 105 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8411 (tm-30) REVERT: A 130 ILE cc_start: 0.9490 (mm) cc_final: 0.9277 (mm) REVERT: B 49 LEU cc_start: 0.9468 (mm) cc_final: 0.8959 (tp) REVERT: B 52 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 63 GLU cc_start: 0.8526 (pp20) cc_final: 0.8157 (pp20) REVERT: B 84 MET cc_start: 0.9359 (mpp) cc_final: 0.9086 (mpp) REVERT: C 74 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9145 (mmtm) REVERT: C 90 ASP cc_start: 0.8768 (t0) cc_final: 0.8433 (t0) REVERT: C 92 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8610 (mt-10) REVERT: C 94 ASN cc_start: 0.9462 (t0) cc_final: 0.9235 (m-40) REVERT: D 62 MET cc_start: 0.9186 (mmm) cc_final: 0.8780 (mmm) REVERT: D 76 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8718 (mm-30) REVERT: D 85 LYS cc_start: 0.9445 (mtpt) cc_final: 0.9035 (mmmt) REVERT: E 50 GLU cc_start: 0.8986 (tp30) cc_final: 0.8014 (tp30) REVERT: E 74 ILE cc_start: 0.9480 (mt) cc_final: 0.9138 (mt) REVERT: E 82 LEU cc_start: 0.8409 (mt) cc_final: 0.8076 (mt) REVERT: E 93 GLN cc_start: 0.8910 (tt0) cc_final: 0.8478 (tt0) REVERT: E 120 MET cc_start: 0.9053 (mmm) cc_final: 0.8549 (mmm) REVERT: F 25 ASN cc_start: 0.9322 (m-40) cc_final: 0.9098 (t0) REVERT: F 63 GLU cc_start: 0.9295 (pt0) cc_final: 0.8813 (pp20) REVERT: F 64 ASN cc_start: 0.9062 (m-40) cc_final: 0.7697 (m-40) REVERT: F 84 MET cc_start: 0.9148 (tpt) cc_final: 0.8741 (tpp) REVERT: H 47 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8949 (tm-30) REVERT: H 49 HIS cc_start: 0.8961 (m-70) cc_final: 0.8644 (m90) REVERT: H 59 MET cc_start: 0.8776 (tpp) cc_final: 0.8442 (tpp) REVERT: H 69 ILE cc_start: 0.9012 (mm) cc_final: 0.8609 (mm) REVERT: H 82 HIS cc_start: 0.9084 (OUTLIER) cc_final: 0.8713 (m90) REVERT: H 109 HIS cc_start: 0.8423 (m90) cc_final: 0.8090 (m90) REVERT: H 113 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8699 (mm-30) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.1244 time to fit residues: 52.3745 Evaluate side-chains 249 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.076397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055635 restraints weight = 83857.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056747 restraints weight = 44961.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.057594 restraints weight = 30295.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058065 restraints weight = 23911.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058422 restraints weight = 21005.295| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15895 Z= 0.163 Angle : 0.694 8.187 22928 Z= 0.410 Chirality : 0.045 0.270 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.819 162.857 4918 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.32 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: 1.26 (0.27), residues: 964 helix: 1.59 (0.20), residues: 626 sheet: -1.18 (1.07), residues: 24 loop : -0.46 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 81 TYR 0.026 0.002 TYR H 40 PHE 0.016 0.001 PHE D 65 TRP 0.016 0.002 TRP O 214 HIS 0.012 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (15895) covalent geometry : angle 0.69421 / 0.41 (22928) hydrogen bonds : bond 0.04694 / 3.00 ( 895) hydrogen bonds : angle 3.51620 / 2.99 ( 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 301 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.388 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 193 LEU cc_start: 0.9165 (tp) cc_final: 0.8560 (tp) REVERT: O 197 TYR cc_start: 0.8719 (m-80) cc_final: 0.8187 (m-80) REVERT: O 201 MET cc_start: 0.7965 (mtm) cc_final: 0.7724 (mpp) REVERT: O 204 PHE cc_start: 0.9099 (m-80) cc_final: 0.8865 (m-80) REVERT: P 181 MET cc_start: 0.3766 (tpt) cc_final: 0.3162 (mmp) REVERT: G 38 ASN cc_start: 0.9048 (t0) cc_final: 0.8840 (t0) REVERT: G 68 ASN cc_start: 0.9609 (m-40) cc_final: 0.9362 (m110) REVERT: G 84 GLN cc_start: 0.8929 (tp40) cc_final: 0.8670 (tp-100) REVERT: G 88 ARG cc_start: 0.8695 (mmt180) cc_final: 0.7564 (mtp180) REVERT: G 100 VAL cc_start: 0.9361 (p) cc_final: 0.8998 (p) REVERT: A 53 ARG cc_start: 0.9597 (ptm-80) cc_final: 0.9297 (ptm160) REVERT: A 54 TYR cc_start: 0.9568 (m-80) cc_final: 0.8650 (m-80) REVERT: A 87 SER cc_start: 0.9155 (p) cc_final: 0.8501 (t) REVERT: A 105 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8431 (tm-30) REVERT: B 31 LYS cc_start: 0.9460 (tmtt) cc_final: 0.9139 (tmtt) REVERT: B 49 LEU cc_start: 0.9473 (mm) cc_final: 0.9010 (tp) REVERT: B 52 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8592 (mp0) REVERT: B 63 GLU cc_start: 0.8593 (pp20) cc_final: 0.8197 (pp20) REVERT: B 68 ASP cc_start: 0.8866 (m-30) cc_final: 0.8663 (m-30) REVERT: B 84 MET cc_start: 0.9354 (mpp) cc_final: 0.9067 (mpp) REVERT: C 74 LYS cc_start: 0.9376 (mmtm) cc_final: 0.9128 (mppt) REVERT: C 90 ASP cc_start: 0.8705 (t0) cc_final: 0.8376 (t0) REVERT: C 94 ASN cc_start: 0.9443 (t0) cc_final: 0.9215 (m-40) REVERT: D 41 VAL cc_start: 0.9496 (m) cc_final: 0.9281 (p) REVERT: D 62 MET cc_start: 0.9110 (mmm) cc_final: 0.8655 (mmm) REVERT: D 85 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9010 (mmmt) REVERT: E 50 GLU cc_start: 0.8958 (tp30) cc_final: 0.8676 (tp30) REVERT: E 120 MET cc_start: 0.9081 (mmm) cc_final: 0.8482 (mmm) REVERT: F 25 ASN cc_start: 0.9357 (m-40) cc_final: 0.9110 (t0) REVERT: F 63 GLU cc_start: 0.9278 (pt0) cc_final: 0.8756 (pp20) REVERT: F 64 ASN cc_start: 0.9039 (m-40) cc_final: 0.7689 (m-40) REVERT: F 66 ILE cc_start: 0.9645 (mm) cc_final: 0.9251 (mt) REVERT: F 84 MET cc_start: 0.9146 (tpt) cc_final: 0.8692 (tpp) REVERT: H 42 TYR cc_start: 0.7603 (t80) cc_final: 0.7262 (t80) REVERT: H 47 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8927 (tm-30) REVERT: H 49 HIS cc_start: 0.8924 (m-70) cc_final: 0.8672 (m90) REVERT: H 69 ILE cc_start: 0.8947 (mm) cc_final: 0.8582 (mm) REVERT: H 109 HIS cc_start: 0.8433 (m90) cc_final: 0.7968 (m90) REVERT: H 113 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8632 (mm-30) REVERT: H 116 LYS cc_start: 0.9390 (pttm) cc_final: 0.9187 (pttm) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1272 time to fit residues: 55.7125 Evaluate side-chains 254 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 0.8980 chunk 32 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.076855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.055838 restraints weight = 83127.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057135 restraints weight = 44581.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057938 restraints weight = 29704.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058410 restraints weight = 23380.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.058717 restraints weight = 20191.834| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15895 Z= 0.156 Angle : 0.701 9.747 22928 Z= 0.412 Chirality : 0.045 0.262 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.785 161.409 4918 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.22 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 1.06 (0.27), residues: 964 helix: 1.42 (0.20), residues: 626 sheet: -1.31 (1.02), residues: 24 loop : -0.50 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 40 TYR 0.074 0.003 TYR O 173 PHE 0.022 0.002 PHE F 61 TRP 0.015 0.002 TRP O 214 HIS 0.015 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (15895) covalent geometry : angle 0.70100 / 0.41 (22928) hydrogen bonds : bond 0.04596 / 2.96 ( 895) hydrogen bonds : angle 3.49866 / 2.95 ( 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 303 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.402 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 193 LEU cc_start: 0.9056 (tp) cc_final: 0.8157 (tp) REVERT: O 197 TYR cc_start: 0.8810 (m-80) cc_final: 0.8228 (m-80) REVERT: O 201 MET cc_start: 0.7920 (mtm) cc_final: 0.7707 (mpp) REVERT: P 181 MET cc_start: 0.3958 (tpt) cc_final: 0.3300 (mmp) REVERT: G 88 ARG cc_start: 0.8718 (mmt180) cc_final: 0.7559 (mtp180) REVERT: G 100 VAL cc_start: 0.9347 (p) cc_final: 0.8993 (p) REVERT: A 50 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8886 (mt-10) REVERT: A 87 SER cc_start: 0.9114 (p) cc_final: 0.8573 (t) REVERT: A 105 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8463 (tm-30) REVERT: A 120 MET cc_start: 0.8496 (mmt) cc_final: 0.7992 (mmm) REVERT: A 130 ILE cc_start: 0.9458 (mm) cc_final: 0.9039 (mm) REVERT: B 31 LYS cc_start: 0.9458 (tmtt) cc_final: 0.9126 (tmtt) REVERT: B 49 LEU cc_start: 0.9474 (mm) cc_final: 0.9004 (tp) REVERT: B 52 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8589 (mp0) REVERT: B 63 GLU cc_start: 0.8597 (pp20) cc_final: 0.8197 (pp20) REVERT: B 84 MET cc_start: 0.9376 (mpp) cc_final: 0.9076 (mpp) REVERT: C 61 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8592 (tm-30) REVERT: C 74 LYS cc_start: 0.9361 (mmtm) cc_final: 0.9109 (mppt) REVERT: C 90 ASP cc_start: 0.8589 (t0) cc_final: 0.8251 (t0) REVERT: C 94 ASN cc_start: 0.9414 (t0) cc_final: 0.9211 (m-40) REVERT: D 34 LYS cc_start: 0.8655 (pptt) cc_final: 0.8373 (mmtp) REVERT: D 41 VAL cc_start: 0.9363 (m) cc_final: 0.9161 (p) REVERT: D 83 TYR cc_start: 0.8093 (m-10) cc_final: 0.7810 (m-10) REVERT: D 85 LYS cc_start: 0.9416 (mtpt) cc_final: 0.8964 (mmmt) REVERT: E 50 GLU cc_start: 0.8955 (tp30) cc_final: 0.8657 (tp30) REVERT: E 74 ILE cc_start: 0.9594 (tp) cc_final: 0.9388 (tp) REVERT: E 105 GLU cc_start: 0.8785 (pp20) cc_final: 0.8265 (pp20) REVERT: E 106 ASP cc_start: 0.9075 (m-30) cc_final: 0.8755 (m-30) REVERT: E 120 MET cc_start: 0.9098 (mmm) cc_final: 0.8548 (mmm) REVERT: E 126 LEU cc_start: 0.9263 (tp) cc_final: 0.8955 (mm) REVERT: F 25 ASN cc_start: 0.9318 (m-40) cc_final: 0.9106 (t0) REVERT: F 63 GLU cc_start: 0.9326 (pt0) cc_final: 0.8891 (pp20) REVERT: F 66 ILE cc_start: 0.9637 (mm) cc_final: 0.9196 (mt) REVERT: F 84 MET cc_start: 0.9109 (tpt) cc_final: 0.8675 (tpp) REVERT: F 87 VAL cc_start: 0.9795 (t) cc_final: 0.9566 (p) REVERT: F 91 LYS cc_start: 0.9257 (pttt) cc_final: 0.8837 (pttm) REVERT: H 47 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8907 (tm-30) REVERT: H 49 HIS cc_start: 0.8901 (m-70) cc_final: 0.8669 (m90) REVERT: H 69 ILE cc_start: 0.8917 (mm) cc_final: 0.8551 (mm) REVERT: H 109 HIS cc_start: 0.8488 (m90) cc_final: 0.8022 (m90) REVERT: H 113 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8587 (mm-30) REVERT: H 116 LYS cc_start: 0.9374 (pttm) cc_final: 0.9173 (pttm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1244 time to fit residues: 55.0806 Evaluate side-chains 251 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3628 r_free = 0.3628 target = 0.075832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.054940 restraints weight = 84859.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056102 restraints weight = 45824.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.056872 restraints weight = 31077.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057362 restraints weight = 24857.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057674 restraints weight = 21701.206| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4594 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= 0.181 Angle : 0.720 12.074 22928 Z= 0.420 Chirality : 0.044 0.239 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.808 160.906 4918 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.27 % 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: 1.00 (0.27), residues: 964 helix: 1.41 (0.21), residues: 624 sheet: -1.38 (1.04), residues: 24 loop : -0.61 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 45 TYR 0.048 0.003 TYR O 173 PHE 0.016 0.002 PHE O 204 TRP 0.017 0.002 TRP O 214 HIS 0.014 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (15895) covalent geometry : angle 0.72007 / 0.42 (22928) hydrogen bonds : bond 0.05213 / 3.37 ( 895) hydrogen bonds : angle 3.67258 / 3.14 ( 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 284 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.380 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: O 201 MET cc_start: 0.8060 (mtm) cc_final: 0.7817 (mpp) REVERT: P 181 MET cc_start: 0.3997 (tpt) cc_final: 0.3334 (mmp) REVERT: G 68 ASN cc_start: 0.9579 (m-40) cc_final: 0.9361 (m110) REVERT: G 88 ARG cc_start: 0.8594 (mmt180) cc_final: 0.7753 (mtp180) REVERT: G 100 VAL cc_start: 0.9356 (p) cc_final: 0.9020 (p) REVERT: A 54 TYR cc_start: 0.9441 (m-80) cc_final: 0.8839 (m-80) REVERT: A 87 SER cc_start: 0.9135 (p) cc_final: 0.8452 (t) REVERT: A 94 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8037 (mt-10) REVERT: A 105 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8365 (tm-30) REVERT: A 120 MET cc_start: 0.8599 (mmt) cc_final: 0.8396 (mmm) REVERT: A 126 LEU cc_start: 0.9739 (tp) cc_final: 0.9505 (mm) REVERT: B 31 LYS cc_start: 0.9466 (tmtt) cc_final: 0.9124 (tmtt) REVERT: B 49 LEU cc_start: 0.9436 (mm) cc_final: 0.8969 (tp) REVERT: B 52 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8590 (mp0) REVERT: B 63 GLU cc_start: 0.8667 (pp20) cc_final: 0.8399 (pp20) REVERT: B 84 MET cc_start: 0.9333 (mpp) cc_final: 0.9085 (mpp) REVERT: C 74 LYS cc_start: 0.9328 (mmtm) cc_final: 0.9108 (mppt) REVERT: C 90 ASP cc_start: 0.8704 (t0) cc_final: 0.8443 (t0) REVERT: D 41 VAL cc_start: 0.9413 (m) cc_final: 0.9212 (p) REVERT: D 62 MET cc_start: 0.9025 (mmm) cc_final: 0.8702 (mmm) REVERT: D 76 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8629 (mm-30) REVERT: D 83 TYR cc_start: 0.8310 (m-10) cc_final: 0.8058 (m-10) REVERT: E 50 GLU cc_start: 0.8860 (tp30) cc_final: 0.8554 (tp30) REVERT: E 93 GLN cc_start: 0.8635 (tt0) cc_final: 0.8434 (tt0) REVERT: E 105 GLU cc_start: 0.8782 (pp20) cc_final: 0.8279 (pp20) REVERT: E 120 MET cc_start: 0.9067 (mmm) cc_final: 0.8482 (mmm) REVERT: E 126 LEU cc_start: 0.9307 (tp) cc_final: 0.8950 (mm) REVERT: E 130 ILE cc_start: 0.8906 (tt) cc_final: 0.8594 (tt) REVERT: F 63 GLU cc_start: 0.9307 (pt0) cc_final: 0.8890 (pp20) REVERT: F 64 ASN cc_start: 0.9350 (t0) cc_final: 0.9084 (t0) REVERT: F 66 ILE cc_start: 0.9617 (mm) cc_final: 0.9209 (mt) REVERT: F 84 MET cc_start: 0.9137 (tpt) cc_final: 0.8690 (tpp) REVERT: H 47 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8970 (tm-30) REVERT: H 69 ILE cc_start: 0.8969 (mm) cc_final: 0.8584 (mm) REVERT: H 109 HIS cc_start: 0.8539 (m90) cc_final: 0.8088 (m90) REVERT: H 113 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8623 (mm-30) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1199 time to fit residues: 50.3002 Evaluate side-chains 242 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 4.9990 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.076333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055425 restraints weight = 83845.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056647 restraints weight = 45083.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057494 restraints weight = 30221.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057969 restraints weight = 23763.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058291 restraints weight = 20527.027| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15895 Z= 0.165 Angle : 0.718 13.798 22928 Z= 0.419 Chirality : 0.044 0.241 2563 Planarity : 0.006 0.096 1719 Dihedral : 30.830 159.615 4918 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.84 (0.27), residues: 964 helix: 1.28 (0.20), residues: 624 sheet: -1.48 (1.02), residues: 24 loop : -0.66 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 45 TYR 0.043 0.003 TYR B 88 PHE 0.025 0.002 PHE F 61 TRP 0.016 0.002 TRP O 214 HIS 0.014 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (15895) covalent geometry : angle 0.71843 / 0.42 (22928) hydrogen bonds : bond 0.04701 / 3.02 ( 895) hydrogen bonds : angle 3.67821 / 3.10 ( 2235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.71 seconds wall clock time: 45 minutes 25.33 seconds (2725.33 seconds total)