Starting phenix.real_space_refine on Wed Jun 3 21:44:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7i_70200/06_2026/9o7i_70200.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 S 18 5.16 5 C 2700 2.51 5 N 756 2.21 5 O 886 1.98 5 H 4184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8544 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 941 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "B" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1144 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'TRANS': 71} Chain: "C" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3258 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Chain: "D" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3201 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 202} Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8544 At special positions: 0 Unit cell: (63.384, 73.392, 110.922, 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 18 16.00 O 886 8.00 N 756 7.00 C 2700 6.00 H 4184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 334.1 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1056 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 10 sheets defined 28.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 159 through 176 removed outlier: 4.059A pdb=" N ARG A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.137A pdb=" N GLY A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 218 removed outlier: 3.658A pdb=" N HIS A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 183 removed outlier: 4.245A pdb=" N ILE B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 218 removed outlier: 3.936A pdb=" N SER B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 114 removed outlier: 4.041A pdb=" N PHE C 114 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 209 through 212 Processing sheet with id=AA1, first strand: chain 'C' and resid 40 through 43 removed outlier: 6.706A pdb=" N LEU C 64 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR C 80 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 66 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 148 removed outlier: 3.727A pdb=" N SER C 207 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 168 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR C 203 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 185 removed outlier: 3.893A pdb=" N TRP C 178 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 60 through 64 removed outlier: 6.838A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D 53 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP D 37 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR D 110 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 104 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N PHE D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 64 removed outlier: 6.838A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG D 53 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP D 37 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.690A pdb=" N SER D 128 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP D 152 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.690A pdb=" N SER D 128 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP D 152 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 162 removed outlier: 4.619A pdb=" N TYR D 202 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 242 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 4179 1.13 - 1.30: 799 1.30 - 1.48: 1720 1.48 - 1.65: 1912 1.65 - 1.82: 23 Bond restraints: 8633 Sorted by residual: bond pdb=" N SER C 37 " pdb=" H SER C 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CZ3 TRP D 50 " pdb=" HZ3 TRP D 50 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N GLY C 95 " pdb=" H GLY C 95 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG C 172 " pdb="HH11 ARG C 172 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASP D 28 " pdb=" H ASP D 28 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 8628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 12983 2.54 - 5.08: 1979 5.08 - 7.62: 513 7.62 - 10.16: 36 10.16 - 12.70: 5 Bond angle restraints: 15516 Sorted by residual: angle pdb=" CA PHE D 154 " pdb=" C PHE D 154 " pdb=" N PRO D 155 " ideal model delta sigma weight residual 117.95 121.88 -3.93 7.70e-01 1.69e+00 2.60e+01 angle pdb=" CB HIS A 162 " pdb=" CG HIS A 162 " pdb=" CD2 HIS A 162 " ideal model delta sigma weight residual 131.20 125.28 5.92 1.30e+00 5.92e-01 2.08e+01 angle pdb=" CB HIS A 192 " pdb=" CG HIS A 192 " pdb=" CD2 HIS A 192 " ideal model delta sigma weight residual 131.20 125.46 5.74 1.30e+00 5.92e-01 1.95e+01 angle pdb=" CB HIS B 156 " pdb=" CG HIS B 156 " pdb=" CD2 HIS B 156 " ideal model delta sigma weight residual 131.20 125.63 5.57 1.30e+00 5.92e-01 1.84e+01 angle pdb=" CB HIS B 204 " pdb=" CG HIS B 204 " pdb=" CD2 HIS B 204 " ideal model delta sigma weight residual 131.20 125.69 5.51 1.30e+00 5.92e-01 1.79e+01 ... (remaining 15511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 3662 14.98 - 29.96: 277 29.96 - 44.94: 96 44.94 - 59.91: 61 59.91 - 74.89: 24 Dihedral angle restraints: 4120 sinusoidal: 2219 harmonic: 1901 Sorted by residual: dihedral pdb=" CA LEU C 165 " pdb=" C LEU C 165 " pdb=" N LEU C 166 " pdb=" CA LEU C 166 " ideal model delta harmonic sigma weight residual 180.00 150.78 29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA LEU D 186 " pdb=" C LEU D 186 " pdb=" N SER D 187 " pdb=" CA SER D 187 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ALA C 82 " pdb=" C ALA C 82 " pdb=" N SER C 83 " pdb=" CA SER C 83 " ideal model delta harmonic sigma weight residual -180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 4117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 326 0.058 - 0.116: 213 0.116 - 0.174: 88 0.174 - 0.232: 33 0.232 - 0.290: 5 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA ASP C 181 " pdb=" N ASP C 181 " pdb=" C ASP C 181 " pdb=" CB ASP C 181 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG D 102 " pdb=" N ARG D 102 " pdb=" C ARG D 102 " pdb=" CB ARG D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA SER C 201 " pdb=" N SER C 201 " pdb=" C SER C 201 " pdb=" CB SER C 201 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 662 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 92 " 0.229 9.50e-02 1.11e+02 1.32e-01 2.67e+02 pdb=" NE ARG C 92 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 92 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG C 92 " 0.121 2.00e-02 2.50e+03 pdb=" NH2 ARG C 92 " 0.028 2.00e-02 2.50e+03 pdb="HH11 ARG C 92 " -0.240 2.00e-02 2.50e+03 pdb="HH12 ARG C 92 " 0.089 2.00e-02 2.50e+03 pdb="HH21 ARG C 92 " -0.103 2.00e-02 2.50e+03 pdb="HH22 ARG C 92 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 102 " -0.234 9.50e-02 1.11e+02 1.14e-01 1.61e+02 pdb=" NE ARG D 102 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG D 102 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 102 " -0.074 2.00e-02 2.50e+03 pdb=" NH2 ARG D 102 " 0.005 2.00e-02 2.50e+03 pdb="HH11 ARG D 102 " 0.180 2.00e-02 2.50e+03 pdb="HH12 ARG D 102 " -0.078 2.00e-02 2.50e+03 pdb="HH21 ARG D 102 " -0.116 2.00e-02 2.50e+03 pdb="HH22 ARG D 102 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 60 " 0.148 2.00e-02 2.50e+03 5.40e-02 1.17e+02 pdb=" CG TRP D 60 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP D 60 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 60 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP D 60 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP D 60 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP D 60 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 60 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 60 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP D 60 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP D 60 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP D 60 " -0.055 2.00e-02 2.50e+03 pdb=" HE3 TRP D 60 " -0.062 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 60 " 0.048 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 60 " -0.025 2.00e-02 2.50e+03 pdb=" HH2 TRP D 60 " 0.077 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 655 2.20 - 2.80: 15311 2.80 - 3.40: 22901 3.40 - 4.00: 30047 4.00 - 4.60: 44603 Nonbonded interactions: 113517 Sorted by model distance: nonbonded pdb=" OE2 GLU C 135 " pdb=" HH TYR C 203 " model vdw 1.605 2.450 nonbonded pdb=" O TYR D 98 " pdb=" HG1 THR D 115 " model vdw 1.609 2.450 nonbonded pdb=" OE2 GLU B 158 " pdb=" HG1 THR C 62 " model vdw 1.611 2.450 nonbonded pdb=" OE1 GLU C 31 " pdb=" HG1 THR C 125 " model vdw 1.632 2.450 nonbonded pdb=" O GLU B 213 " pdb=" HG SER B 216 " model vdw 1.636 2.450 ... (remaining 113512 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.180 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 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 : 0.012 0.037 4449 Z= 0.765 Angle : 1.809 7.772 6031 Z= 1.193 Chirality : 0.089 0.290 665 Planarity : 0.014 0.117 788 Dihedral : 13.289 74.893 1631 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.50 % Favored : 92.96 % Rotamer: Outliers : 0.41 % Allowed : 3.09 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -1.20 (0.34), residues: 554 helix: -0.54 (0.40), residues: 120 sheet: -0.49 (0.38), residues: 162 loop : -1.01 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 41 TYR 0.097 0.020 TYR D 98 PHE 0.080 0.012 PHE D 174 TRP 0.097 0.029 TRP D 60 HIS 0.012 0.004 HIS D 208 Details of bonding type rmsd/Z covalent geometry : bond 0.01244 / 0.77 ( 4449) covalent geometry : angle 1.80935 / 1.19 ( 6031) hydrogen bonds : bond 0.15153 / 10.52 ( 212) hydrogen bonds : angle 8.09413 / 6.02 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.287 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: B 157 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8221 (mp10) REVERT: D 205 ASN cc_start: 0.6242 (m110) cc_final: 0.5994 (m-40) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.2296 time to fit residues: 36.2772 Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 GLN C 168 ASN D 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.192523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.153149 restraints weight = 17079.746| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.02 r_work: 0.3958 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4449 Z= 0.180 Angle : 0.705 8.699 6031 Z= 0.373 Chirality : 0.041 0.141 665 Planarity : 0.005 0.042 788 Dihedral : 6.934 40.460 613 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 1.85 % Allowed : 8.85 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.81 (0.35), residues: 554 helix: 0.91 (0.45), residues: 126 sheet: -0.42 (0.37), residues: 177 loop : -1.33 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 54 TYR 0.015 0.002 TYR C 222 PHE 0.015 0.002 PHE C 114 TRP 0.015 0.002 TRP D 50 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 4449) covalent geometry : angle 0.70478 / 0.37 ( 6031) hydrogen bonds : bond 0.04496 / 3.12 ( 212) hydrogen bonds : angle 5.93308 / 4.46 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.265 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: A 163 SER cc_start: 0.8603 (t) cc_final: 0.8257 (p) REVERT: A 176 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8544 (mm-30) REVERT: A 179 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 100 THR cc_start: 0.9050 (p) cc_final: 0.8667 (t) REVERT: C 101 ASP cc_start: 0.7648 (t70) cc_final: 0.7363 (t70) REVERT: D 210 PRO cc_start: 0.7202 (Cg_exo) cc_final: 0.6847 (Cg_endo) outliers start: 9 outliers final: 8 residues processed: 94 average time/residue: 0.2238 time to fit residues: 25.0090 Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 214 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 33 optimal weight: 0.0870 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.182482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142128 restraints weight = 16911.857| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.17 r_work: 0.3813 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4449 Z= 0.134 Angle : 0.617 7.190 6031 Z= 0.327 Chirality : 0.040 0.140 665 Planarity : 0.005 0.041 788 Dihedral : 6.163 35.035 613 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.14 % Favored : 93.68 % Rotamer: Outliers : 1.03 % Allowed : 11.11 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.51 (0.36), residues: 554 helix: 1.69 (0.45), residues: 123 sheet: -0.35 (0.38), residues: 180 loop : -1.35 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 194 TYR 0.022 0.001 TYR C 203 PHE 0.012 0.001 PHE D 174 TRP 0.011 0.002 TRP D 50 HIS 0.003 0.001 HIS C 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4449) covalent geometry : angle 0.61675 / 0.33 ( 6031) hydrogen bonds : bond 0.03665 / 2.54 ( 212) hydrogen bonds : angle 5.40069 / 4.10 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.242 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: A 163 SER cc_start: 0.8634 (t) cc_final: 0.8249 (p) REVERT: A 176 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8436 (tp30) REVERT: C 100 THR cc_start: 0.9147 (p) cc_final: 0.8772 (t) REVERT: C 101 ASP cc_start: 0.7751 (t70) cc_final: 0.7520 (t70) REVERT: C 102 PHE cc_start: 0.6775 (m-80) cc_final: 0.6508 (m-80) REVERT: D 210 PRO cc_start: 0.7223 (Cg_exo) cc_final: 0.6872 (Cg_endo) outliers start: 5 outliers final: 5 residues processed: 87 average time/residue: 0.2296 time to fit residues: 23.6400 Evaluate side-chains 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 HIS ** 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 = 0.4357 r_free = 0.4357 target = 0.179078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.138716 restraints weight = 17312.501| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.12 r_work: 0.3779 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4449 Z= 0.176 Angle : 0.625 6.803 6031 Z= 0.329 Chirality : 0.040 0.134 665 Planarity : 0.005 0.036 788 Dihedral : 5.968 33.848 613 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 2.06 % Allowed : 11.73 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.55 (0.36), residues: 554 helix: 2.00 (0.45), residues: 123 sheet: -0.48 (0.39), residues: 183 loop : -1.50 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 102 TYR 0.027 0.002 TYR C 203 PHE 0.012 0.002 PHE C 114 TRP 0.011 0.002 TRP D 50 HIS 0.002 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 4449) covalent geometry : angle 0.62538 / 0.33 ( 6031) hydrogen bonds : bond 0.03535 / 2.42 ( 212) hydrogen bonds : angle 5.33238 / 4.08 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.242 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: A 163 SER cc_start: 0.8684 (t) cc_final: 0.8256 (p) REVERT: A 194 ARG cc_start: 0.8416 (ptp-170) cc_final: 0.8188 (ptp90) REVERT: C 100 THR cc_start: 0.9195 (p) cc_final: 0.8820 (t) REVERT: C 101 ASP cc_start: 0.7817 (t70) cc_final: 0.7570 (t70) REVERT: C 102 PHE cc_start: 0.6829 (m-80) cc_final: 0.6592 (m-80) REVERT: D 210 PRO cc_start: 0.7259 (Cg_exo) cc_final: 0.6907 (Cg_endo) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.1984 time to fit residues: 20.8022 Evaluate side-chains 85 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain D residue 214 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 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 = 0.4351 r_free = 0.4351 target = 0.178979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138370 restraints weight = 17053.101| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.17 r_work: 0.3777 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4449 Z= 0.154 Angle : 0.598 6.712 6031 Z= 0.315 Chirality : 0.039 0.137 665 Planarity : 0.005 0.049 788 Dihedral : 5.662 32.328 613 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 1.85 % Allowed : 12.14 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.51 (0.36), residues: 554 helix: 2.25 (0.47), residues: 123 sheet: -0.54 (0.39), residues: 183 loop : -1.52 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.013 0.001 TYR C 203 PHE 0.010 0.002 PHE A 215 TRP 0.009 0.002 TRP D 50 HIS 0.002 0.000 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 4449) covalent geometry : angle 0.59802 / 0.31 ( 6031) hydrogen bonds : bond 0.03262 / 2.23 ( 212) hydrogen bonds : angle 5.11347 / 3.93 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.247 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: A 163 SER cc_start: 0.8672 (t) cc_final: 0.8289 (p) REVERT: C 100 THR cc_start: 0.9193 (p) cc_final: 0.8751 (t) REVERT: C 101 ASP cc_start: 0.7769 (t70) cc_final: 0.7524 (t70) REVERT: C 102 PHE cc_start: 0.6856 (m-80) cc_final: 0.6240 (m-80) REVERT: D 210 PRO cc_start: 0.7264 (Cg_exo) cc_final: 0.6893 (Cg_endo) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.2151 time to fit residues: 21.3545 Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN ** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 212 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 = 0.4352 r_free = 0.4352 target = 0.179437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.139026 restraints weight = 17103.504| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 3.16 r_work: 0.3770 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4449 Z= 0.130 Angle : 0.566 6.708 6031 Z= 0.297 Chirality : 0.039 0.134 665 Planarity : 0.004 0.039 788 Dihedral : 5.387 31.026 613 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.78 % Favored : 94.04 % Rotamer: Outliers : 2.26 % Allowed : 12.14 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.40 (0.36), residues: 554 helix: 2.49 (0.48), residues: 121 sheet: -0.48 (0.39), residues: 183 loop : -1.49 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.011 0.001 TYR C 203 PHE 0.010 0.001 PHE D 174 TRP 0.008 0.001 TRP D 50 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 4449) covalent geometry : angle 0.56556 / 0.30 ( 6031) hydrogen bonds : bond 0.03076 / 2.09 ( 212) hydrogen bonds : angle 4.92284 / 3.79 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.270 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: A 163 SER cc_start: 0.8650 (t) cc_final: 0.8259 (p) REVERT: A 194 ARG cc_start: 0.8518 (ptp-170) cc_final: 0.8288 (ptp90) REVERT: C 100 THR cc_start: 0.9182 (p) cc_final: 0.8730 (t) REVERT: C 101 ASP cc_start: 0.7729 (t70) cc_final: 0.7457 (t70) REVERT: C 102 PHE cc_start: 0.6905 (m-80) cc_final: 0.6254 (m-80) REVERT: D 210 PRO cc_start: 0.7191 (Cg_exo) cc_final: 0.6817 (Cg_endo) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.2082 time to fit residues: 21.6226 Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS ** C 219 HIS ** 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 = 0.4343 r_free = 0.4343 target = 0.178689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.138363 restraints weight = 17317.531| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 3.11 r_work: 0.3773 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4449 Z= 0.142 Angle : 0.570 6.708 6031 Z= 0.300 Chirality : 0.039 0.135 665 Planarity : 0.005 0.045 788 Dihedral : 5.317 30.244 613 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 2.26 % Allowed : 13.17 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.44 (0.36), residues: 554 helix: 2.29 (0.47), residues: 122 sheet: -0.47 (0.39), residues: 184 loop : -1.48 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.009 0.001 TYR C 203 PHE 0.008 0.001 PHE D 174 TRP 0.007 0.001 TRP D 50 HIS 0.002 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 4449) covalent geometry : angle 0.56994 / 0.30 ( 6031) hydrogen bonds : bond 0.03088 / 2.08 ( 212) hydrogen bonds : angle 4.87664 / 3.75 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.225 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: A 163 SER cc_start: 0.8705 (t) cc_final: 0.8288 (p) REVERT: C 100 THR cc_start: 0.9183 (p) cc_final: 0.8737 (t) REVERT: C 101 ASP cc_start: 0.7722 (t70) cc_final: 0.7460 (t70) REVERT: C 102 PHE cc_start: 0.6901 (m-80) cc_final: 0.6273 (m-80) REVERT: D 210 PRO cc_start: 0.7225 (Cg_exo) cc_final: 0.6836 (Cg_endo) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.2027 time to fit residues: 20.5882 Evaluate side-chains 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 HIS ** 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 = 0.4327 r_free = 0.4327 target = 0.177136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136772 restraints weight = 17092.318| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.05 r_work: 0.3749 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4449 Z= 0.159 Angle : 0.580 6.729 6031 Z= 0.306 Chirality : 0.039 0.140 665 Planarity : 0.005 0.039 788 Dihedral : 5.349 30.185 613 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.86 % Favored : 92.96 % Rotamer: Outliers : 2.06 % Allowed : 13.37 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.54 (0.36), residues: 554 helix: 2.31 (0.47), residues: 121 sheet: -0.53 (0.39), residues: 184 loop : -1.58 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.008 0.001 TYR C 126 PHE 0.010 0.002 PHE C 169 TRP 0.011 0.002 TRP D 37 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 4449) covalent geometry : angle 0.58017 / 0.31 ( 6031) hydrogen bonds : bond 0.03143 / 2.10 ( 212) hydrogen bonds : angle 4.86010 / 3.73 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.250 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: A 163 SER cc_start: 0.8708 (t) cc_final: 0.8260 (p) REVERT: A 194 ARG cc_start: 0.8552 (ptp-170) cc_final: 0.8331 (ptp90) REVERT: C 100 THR cc_start: 0.9167 (p) cc_final: 0.8745 (t) REVERT: C 101 ASP cc_start: 0.7765 (t70) cc_final: 0.7530 (t70) REVERT: C 102 PHE cc_start: 0.6919 (m-80) cc_final: 0.6343 (m-80) REVERT: D 210 PRO cc_start: 0.7251 (Cg_exo) cc_final: 0.6847 (Cg_endo) outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.2118 time to fit residues: 19.6199 Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 6 optimal weight: 0.0000 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 HIS ** 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 = 0.4338 r_free = 0.4338 target = 0.177994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138022 restraints weight = 17017.296| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.07 r_work: 0.3773 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4449 Z= 0.127 Angle : 0.557 6.765 6031 Z= 0.293 Chirality : 0.039 0.137 665 Planarity : 0.005 0.071 788 Dihedral : 5.205 29.887 613 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.50 % Favored : 93.32 % Rotamer: Outliers : 1.85 % Allowed : 13.58 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.46 (0.36), residues: 554 helix: 2.38 (0.47), residues: 121 sheet: -0.50 (0.38), residues: 184 loop : -1.53 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 54 TYR 0.009 0.001 TYR C 203 PHE 0.010 0.001 PHE D 174 TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 4449) covalent geometry : angle 0.55729 / 0.29 ( 6031) hydrogen bonds : bond 0.02970 / 1.97 ( 212) hydrogen bonds : angle 4.74705 / 3.65 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.253 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: A 163 SER cc_start: 0.8703 (t) cc_final: 0.8248 (p) REVERT: A 194 ARG cc_start: 0.8529 (ptp-170) cc_final: 0.8304 (ptp90) REVERT: C 100 THR cc_start: 0.9175 (p) cc_final: 0.8769 (t) REVERT: C 101 ASP cc_start: 0.7759 (t70) cc_final: 0.7517 (t70) REVERT: C 102 PHE cc_start: 0.6967 (m-80) cc_final: 0.6314 (m-80) REVERT: D 210 PRO cc_start: 0.7198 (Cg_exo) cc_final: 0.6805 (Cg_endo) outliers start: 9 outliers final: 9 residues processed: 78 average time/residue: 0.2264 time to fit residues: 20.9997 Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 HIS ** 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 = 0.4339 r_free = 0.4339 target = 0.177759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137563 restraints weight = 17205.227| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.06 r_work: 0.3771 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4449 Z= 0.136 Angle : 0.558 6.754 6031 Z= 0.294 Chirality : 0.039 0.135 665 Planarity : 0.005 0.053 788 Dihedral : 5.134 29.742 613 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 1.85 % Allowed : 13.79 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.47 (0.36), residues: 554 helix: 2.36 (0.47), residues: 121 sheet: -0.48 (0.38), residues: 184 loop : -1.55 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 54 TYR 0.009 0.001 TYR A 164 PHE 0.009 0.001 PHE D 174 TRP 0.007 0.001 TRP D 37 HIS 0.002 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4449) covalent geometry : angle 0.55784 / 0.29 ( 6031) hydrogen bonds : bond 0.03019 / 2.01 ( 212) hydrogen bonds : angle 4.74029 / 3.64 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 12 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.249 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: A 163 SER cc_start: 0.8700 (t) cc_final: 0.8245 (p) REVERT: A 194 ARG cc_start: 0.8568 (ptp-170) cc_final: 0.8338 (ptp90) REVERT: C 100 THR cc_start: 0.9170 (p) cc_final: 0.8749 (t) REVERT: C 101 ASP cc_start: 0.7757 (t70) cc_final: 0.7501 (t70) REVERT: C 102 PHE cc_start: 0.6976 (m-80) cc_final: 0.6319 (m-80) REVERT: D 210 PRO cc_start: 0.7182 (Cg_exo) cc_final: 0.6790 (Cg_endo) outliers start: 9 outliers final: 9 residues processed: 80 average time/residue: 0.2221 time to fit residues: 21.1307 Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 205 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 17 optimal weight: 0.3980 chunk 50 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 HIS ** 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 = 0.4354 r_free = 0.4354 target = 0.179513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139700 restraints weight = 17005.971| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.05 r_work: 0.3783 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4449 Z= 0.109 Angle : 0.537 6.805 6031 Z= 0.282 Chirality : 0.038 0.132 665 Planarity : 0.005 0.056 788 Dihedral : 4.987 29.313 613 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.23 % Allowed : 14.61 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.37 (0.37), residues: 554 helix: 2.37 (0.46), residues: 123 sheet: -0.44 (0.40), residues: 179 loop : -1.42 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 54 TYR 0.011 0.001 TYR C 203 PHE 0.012 0.001 PHE D 174 TRP 0.008 0.001 TRP D 50 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 4449) covalent geometry : angle 0.53707 / 0.28 ( 6031) hydrogen bonds : bond 0.02846 / 1.89 ( 212) hydrogen bonds : angle 4.60632 / 3.55 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.61 seconds wall clock time: 45 minutes 23.05 seconds (2723.05 seconds total)