Starting phenix.real_space_refine on Tue Feb 3 17:03:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ptm_71842/02_2026/9ptm_71842.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ptm_71842/02_2026/9ptm_71842.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/9ptm_71842/02_2026/9ptm_71842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ptm_71842/02_2026/9ptm_71842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ptm_71842/02_2026/9ptm_71842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ptm_71842/02_2026/9ptm_71842.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= 0.131 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 3299 2.51 5 N 870 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5250 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2052 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 262} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 84 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "I" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1586 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 194} Chain: "M" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1528 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 189} Time building chain proxies: 1.02, per 1000 atoms: 0.19 Number of scatterers: 5250 At special positions: 0 Unit cell: (66.316, 83.176, 146.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1063 8.00 N 870 7.00 C 3299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 198 " distance=2.02 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 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: 0.25 Conformation dependent library (CDL) restraints added in 200.4 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 6.0% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 38 through 41 No H-bonds generated for 'chain 'A' and resid 38 through 41' Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 66 through 69 removed outlier: 3.662A pdb=" N SER A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'I' and resid 27 through 31 removed outlier: 4.143A pdb=" N TYR I 31 " --> pdb=" O PHE I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 89 Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.503A pdb=" N ILE M 83 " --> pdb=" O GLN M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 127 removed outlier: 3.530A pdb=" N LEU M 125 " --> pdb=" O SER M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 187 removed outlier: 3.719A pdb=" N GLU M 187 " --> pdb=" O LYS M 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.656A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 142 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG A 132 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 144 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 130 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP A 146 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL A 128 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 148 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 124 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.656A pdb=" N ALA A 18 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TYR A 149 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 20 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE A 142 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ARG A 132 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 144 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE A 130 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP A 146 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL A 128 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE A 148 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 124 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.525A pdb=" N VAL A 27 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 107 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 37 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 105 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 74 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.376A pdb=" N VAL A 168 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASN G 8 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL A 170 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N LYS G 10 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY A 241 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR A 195 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 239 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU A 197 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR A 237 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 178 through 180 Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 5 Processing sheet with id=AB1, first strand: chain 'I' and resid 9 through 11 removed outlier: 6.772A pdb=" N ILE I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR I 49 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 123 through 127 removed outlier: 4.002A pdb=" N GLY I 142 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR I 178 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 123 through 127 removed outlier: 4.002A pdb=" N GLY I 142 " --> pdb=" O LEU I 127 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR I 178 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 154 through 157 Processing sheet with id=AB5, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.451A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.816A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 129 through 139 removed outlier: 5.177A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 153 through 154 204 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1686 1.34 - 1.46: 1174 1.46 - 1.57: 2488 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5372 Sorted by residual: bond pdb=" N PHE A 1 " pdb=" CA PHE A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLU I 0 " pdb=" CA GLU I 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N ASP M 1 " pdb=" CA ASP M 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.36e+00 bond pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 1.532 1.522 0.010 6.50e-03 2.37e+04 2.33e+00 ... (remaining 5367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 6575 0.98 - 1.96: 625 1.96 - 2.94: 97 2.94 - 3.92: 43 3.92 - 4.91: 9 Bond angle restraints: 7349 Sorted by residual: angle pdb=" N SER I 205 " pdb=" CA SER I 205 " pdb=" C SER I 205 " ideal model delta sigma weight residual 114.56 110.23 4.33 1.27e+00 6.20e-01 1.16e+01 angle pdb=" N VAL A 35 " pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 111.48 108.59 2.89 9.40e-01 1.13e+00 9.44e+00 angle pdb=" N GLN A 41 " pdb=" CA GLN A 41 " pdb=" C GLN A 41 " ideal model delta sigma weight residual 111.56 115.30 -3.74 1.38e+00 5.25e-01 7.36e+00 angle pdb=" N VAL I 196 " pdb=" CA VAL I 196 " pdb=" C VAL I 196 " ideal model delta sigma weight residual 106.55 110.23 -3.68 1.45e+00 4.76e-01 6.45e+00 angle pdb=" N GLY A 205 " pdb=" CA GLY A 205 " pdb=" C GLY A 205 " ideal model delta sigma weight residual 115.62 111.61 4.01 1.71e+00 3.42e-01 5.50e+00 ... (remaining 7344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 2854 17.67 - 35.34: 229 35.34 - 53.00: 56 53.00 - 70.67: 18 70.67 - 88.34: 7 Dihedral angle restraints: 3164 sinusoidal: 1156 harmonic: 2008 Sorted by residual: dihedral pdb=" CB CYS M 23 " pdb=" SG CYS M 23 " pdb=" SG CYS M 88 " pdb=" CB CYS M 88 " ideal model delta sinusoidal sigma weight residual 93.00 154.06 -61.06 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CA ASN A 136 " pdb=" C ASN A 136 " pdb=" N TYR A 137 " pdb=" CA TYR A 137 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR A 137 " pdb=" C TYR A 137 " pdb=" N ASN A 138 " pdb=" CA ASN A 138 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 3161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 450 0.028 - 0.056: 236 0.056 - 0.084: 80 0.084 - 0.112: 56 0.112 - 0.140: 26 Chirality restraints: 848 Sorted by residual: chirality pdb=" CA ILE A 130 " pdb=" N ILE A 130 " pdb=" C ILE A 130 " pdb=" CB ILE A 130 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE A 272 " pdb=" N ILE A 272 " pdb=" C ILE A 272 " pdb=" CB ILE A 272 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 845 not shown) Planarity restraints: 945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 175 " -0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO A 176 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 151 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO I 152 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO I 152 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 152 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 90 " -0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 91 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " -0.023 5.00e-02 4.00e+02 ... (remaining 942 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1111 2.78 - 3.31: 4871 3.31 - 3.84: 8289 3.84 - 4.37: 10009 4.37 - 4.90: 17871 Nonbonded interactions: 42151 Sorted by model distance: nonbonded pdb=" OG1 THR M 182 " pdb=" OD1 ASP M 184 " model vdw 2.244 3.040 nonbonded pdb=" O ASP M 170 " pdb=" OG SER M 171 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP M 167 " pdb=" N ASP M 170 " model vdw 2.249 3.120 nonbonded pdb=" O SER I 84 " pdb=" OG SER I 84 " model vdw 2.258 3.040 nonbonded pdb=" O GLY M 68 " pdb=" OG1 THR M 69 " model vdw 2.285 3.040 ... (remaining 42146 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: 9.120 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.004 0.033 5378 Z= 0.201 Angle : 0.668 4.906 7361 Z= 0.390 Chirality : 0.046 0.140 848 Planarity : 0.005 0.049 945 Dihedral : 15.214 88.340 1870 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.51 % Allowed : 20.17 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.31), residues: 688 helix: -1.62 (1.96), residues: 7 sheet: -0.68 (0.28), residues: 290 loop : -0.65 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 166 TYR 0.013 0.002 TYR M 192 PHE 0.017 0.002 PHE A 209 TRP 0.010 0.002 TRP I 35 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5372) covalent geometry : angle 0.66743 ( 7349) SS BOND : bond 0.00582 ( 6) SS BOND : angle 0.91101 ( 12) hydrogen bonds : bond 0.25148 ( 183) hydrogen bonds : angle 11.91925 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 80 SER cc_start: 0.8972 (t) cc_final: 0.8714 (m) REVERT: A 174 ASP cc_start: 0.7560 (m-30) cc_final: 0.7166 (m-30) REVERT: A 262 GLN cc_start: 0.7683 (tt0) cc_final: 0.7436 (tp40) REVERT: I 49 TYR cc_start: 0.7318 (p90) cc_final: 0.7052 (p90) REVERT: I 56 ASP cc_start: 0.8600 (m-30) cc_final: 0.8156 (m-30) REVERT: M 83 ILE cc_start: 0.8260 (mp) cc_final: 0.8030 (mm) REVERT: M 192 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.4908 (m-80) outliers start: 3 outliers final: 2 residues processed: 135 average time/residue: 0.0657 time to fit residues: 11.5406 Evaluate side-chains 125 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain M residue 192 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 143 GLN I 5 GLN I 174 GLN M 55 HIS M 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131556 restraints weight = 6352.948| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.64 r_work: 0.3324 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5378 Z= 0.168 Angle : 0.663 6.971 7361 Z= 0.354 Chirality : 0.049 0.153 848 Planarity : 0.005 0.049 945 Dihedral : 6.568 57.109 761 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.93 % Allowed : 15.93 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.59 (0.32), residues: 688 helix: -1.05 (1.84), residues: 8 sheet: -0.24 (0.30), residues: 285 loop : -0.41 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 98 TYR 0.016 0.002 TYR A 175 PHE 0.018 0.002 PHE A 209 TRP 0.013 0.002 TRP I 35 HIS 0.002 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5372) covalent geometry : angle 0.66190 ( 7349) SS BOND : bond 0.00539 ( 6) SS BOND : angle 0.99091 ( 12) hydrogen bonds : bond 0.03715 ( 183) hydrogen bonds : angle 7.35467 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.133 Fit side-chains REVERT: A 80 SER cc_start: 0.8871 (t) cc_final: 0.8594 (m) REVERT: A 112 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 174 ASP cc_start: 0.7607 (m-30) cc_final: 0.7179 (m-30) REVERT: I 2 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: I 56 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: M 83 ILE cc_start: 0.8238 (mp) cc_final: 0.7933 (mm) outliers start: 35 outliers final: 21 residues processed: 141 average time/residue: 0.0609 time to fit residues: 11.2829 Evaluate side-chains 147 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN I 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127924 restraints weight = 6384.796| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.65 r_work: 0.3273 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5378 Z= 0.271 Angle : 0.726 7.529 7361 Z= 0.388 Chirality : 0.051 0.161 848 Planarity : 0.005 0.050 945 Dihedral : 6.985 58.322 759 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 6.61 % Allowed : 17.97 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.64 (0.32), residues: 688 helix: -1.74 (1.29), residues: 8 sheet: -0.22 (0.29), residues: 284 loop : -0.47 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 197 TYR 0.024 0.003 TYR M 192 PHE 0.021 0.003 PHE A 209 TRP 0.015 0.003 TRP I 35 HIS 0.005 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 5372) covalent geometry : angle 0.72504 ( 7349) SS BOND : bond 0.00837 ( 6) SS BOND : angle 1.09649 ( 12) hydrogen bonds : bond 0.04090 ( 183) hydrogen bonds : angle 7.27746 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 80 SER cc_start: 0.8938 (t) cc_final: 0.8685 (m) REVERT: A 174 ASP cc_start: 0.7615 (m-30) cc_final: 0.7267 (m-30) REVERT: I 2 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7499 (mt0) REVERT: I 56 ASP cc_start: 0.8281 (m-30) cc_final: 0.8078 (m-30) outliers start: 39 outliers final: 33 residues processed: 145 average time/residue: 0.0596 time to fit residues: 11.4365 Evaluate side-chains 156 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Chi-restraints excluded: chain M residue 178 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.0770 chunk 37 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN I 5 GLN I 38 GLN M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131656 restraints weight = 6319.439| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.67 r_work: 0.3331 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5378 Z= 0.147 Angle : 0.599 6.479 7361 Z= 0.319 Chirality : 0.047 0.147 848 Planarity : 0.005 0.047 945 Dihedral : 6.307 57.298 759 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.92 % Allowed : 20.51 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.53 (0.31), residues: 688 helix: -1.16 (1.49), residues: 8 sheet: -0.22 (0.29), residues: 290 loop : -0.34 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.012 0.002 TYR M 192 PHE 0.017 0.002 PHE A 209 TRP 0.012 0.001 TRP I 35 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5372) covalent geometry : angle 0.59872 ( 7349) SS BOND : bond 0.00536 ( 6) SS BOND : angle 0.62413 ( 12) hydrogen bonds : bond 0.03031 ( 183) hydrogen bonds : angle 6.50815 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 80 SER cc_start: 0.8897 (t) cc_final: 0.8661 (m) REVERT: A 174 ASP cc_start: 0.7698 (m-30) cc_final: 0.7312 (m-30) REVERT: I 2 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7350 (mt0) REVERT: M 27 GLN cc_start: 0.7844 (pt0) cc_final: 0.7569 (pt0) outliers start: 29 outliers final: 22 residues processed: 144 average time/residue: 0.0549 time to fit residues: 10.4509 Evaluate side-chains 143 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 51 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 17 optimal weight: 0.4980 chunk 45 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.0060 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.0060 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 57 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 overall best weight: 0.1308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN I 5 GLN I 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.135099 restraints weight = 6356.758| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.70 r_work: 0.3371 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5378 Z= 0.103 Angle : 0.539 6.539 7361 Z= 0.289 Chirality : 0.045 0.142 848 Planarity : 0.004 0.045 945 Dihedral : 5.655 55.616 759 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.58 % Allowed : 19.83 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.25 (0.32), residues: 688 helix: -0.56 (1.61), residues: 8 sheet: 0.05 (0.29), residues: 278 loop : -0.23 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.017 0.001 TYR A 175 PHE 0.013 0.002 PHE A 209 TRP 0.011 0.001 TRP I 191 HIS 0.002 0.000 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5372) covalent geometry : angle 0.53950 ( 7349) SS BOND : bond 0.00375 ( 6) SS BOND : angle 0.40147 ( 12) hydrogen bonds : bond 0.02624 ( 183) hydrogen bonds : angle 5.88865 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 80 SER cc_start: 0.8812 (t) cc_final: 0.8602 (m) REVERT: I 2 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: I 60 ASN cc_start: 0.8319 (t0) cc_final: 0.8036 (t0) outliers start: 27 outliers final: 20 residues processed: 138 average time/residue: 0.0647 time to fit residues: 11.5605 Evaluate side-chains 141 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 7 optimal weight: 0.1980 chunk 63 optimal weight: 0.0010 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.153973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132977 restraints weight = 6386.251| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.69 r_work: 0.3337 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5378 Z= 0.142 Angle : 0.569 7.863 7361 Z= 0.302 Chirality : 0.046 0.146 848 Planarity : 0.004 0.045 945 Dihedral : 5.540 52.108 755 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 6.27 % Allowed : 18.98 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.19 (0.32), residues: 688 helix: -0.42 (1.69), residues: 8 sheet: 0.13 (0.29), residues: 278 loop : -0.23 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.011 0.002 TYR A 196 PHE 0.013 0.002 PHE A 209 TRP 0.011 0.002 TRP I 35 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5372) covalent geometry : angle 0.56944 ( 7349) SS BOND : bond 0.00507 ( 6) SS BOND : angle 0.54035 ( 12) hydrogen bonds : bond 0.02828 ( 183) hydrogen bonds : angle 5.95742 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7391 (m-40) cc_final: 0.6941 (m-40) REVERT: A 80 SER cc_start: 0.8877 (t) cc_final: 0.8640 (m) REVERT: I 2 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: I 60 ASN cc_start: 0.8399 (t0) cc_final: 0.8111 (t0) REVERT: M 166 GLN cc_start: 0.7380 (tt0) cc_final: 0.6867 (tt0) outliers start: 37 outliers final: 32 residues processed: 147 average time/residue: 0.0611 time to fit residues: 11.8521 Evaluate side-chains 157 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.151676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130799 restraints weight = 6388.824| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.67 r_work: 0.3314 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5378 Z= 0.185 Angle : 0.610 7.263 7361 Z= 0.324 Chirality : 0.047 0.152 848 Planarity : 0.005 0.049 945 Dihedral : 5.747 47.923 755 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.93 % Allowed : 20.51 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.27 (0.32), residues: 688 helix: -0.90 (1.56), residues: 8 sheet: 0.08 (0.29), residues: 287 loop : -0.28 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 197 TYR 0.015 0.002 TYR I 148 PHE 0.017 0.002 PHE A 209 TRP 0.011 0.002 TRP I 35 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5372) covalent geometry : angle 0.60956 ( 7349) SS BOND : bond 0.00624 ( 6) SS BOND : angle 0.69139 ( 12) hydrogen bonds : bond 0.03067 ( 183) hydrogen bonds : angle 6.20320 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7388 (m-40) cc_final: 0.6969 (m-40) REVERT: A 80 SER cc_start: 0.8929 (t) cc_final: 0.8667 (m) REVERT: A 162 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: I 2 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: M 166 GLN cc_start: 0.7485 (tt0) cc_final: 0.7123 (tt0) outliers start: 35 outliers final: 30 residues processed: 149 average time/residue: 0.0603 time to fit residues: 11.7259 Evaluate side-chains 159 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 205 SER Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 117 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 64 optimal weight: 0.0060 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.0060 chunk 58 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN I 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134332 restraints weight = 6301.772| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.62 r_work: 0.3351 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5378 Z= 0.114 Angle : 0.542 7.131 7361 Z= 0.289 Chirality : 0.045 0.135 848 Planarity : 0.004 0.045 945 Dihedral : 4.989 24.936 752 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.92 % Allowed : 21.19 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.05 (0.32), residues: 688 helix: -0.52 (1.67), residues: 8 sheet: 0.27 (0.29), residues: 284 loop : -0.16 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 98 TYR 0.009 0.001 TYR A 196 PHE 0.014 0.002 PHE A 209 TRP 0.011 0.001 TRP M 163 HIS 0.002 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5372) covalent geometry : angle 0.54207 ( 7349) SS BOND : bond 0.00421 ( 6) SS BOND : angle 0.42312 ( 12) hydrogen bonds : bond 0.02629 ( 183) hydrogen bonds : angle 5.77764 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7392 (m-40) cc_final: 0.7032 (m-40) REVERT: A 162 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: I 2 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: I 60 ASN cc_start: 0.8384 (t0) cc_final: 0.8144 (t0) outliers start: 29 outliers final: 25 residues processed: 141 average time/residue: 0.0548 time to fit residues: 10.1232 Evaluate side-chains 145 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 45 GLU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 2 optimal weight: 0.0980 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 49 optimal weight: 0.4980 overall best weight: 0.2618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132963 restraints weight = 6373.292| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.69 r_work: 0.3337 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5378 Z= 0.141 Angle : 0.561 6.794 7361 Z= 0.297 Chirality : 0.046 0.146 848 Planarity : 0.004 0.048 945 Dihedral : 5.070 24.274 752 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.25 % Allowed : 21.36 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.03 (0.32), residues: 688 helix: -0.62 (1.61), residues: 8 sheet: 0.31 (0.29), residues: 287 loop : -0.18 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 98 TYR 0.019 0.002 TYR A 175 PHE 0.014 0.002 PHE A 209 TRP 0.012 0.002 TRP M 163 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5372) covalent geometry : angle 0.56086 ( 7349) SS BOND : bond 0.00510 ( 6) SS BOND : angle 0.51198 ( 12) hydrogen bonds : bond 0.02748 ( 183) hydrogen bonds : angle 5.84424 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7410 (m-40) cc_final: 0.6997 (m-40) REVERT: A 162 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: I 2 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7387 (mt0) REVERT: I 60 ASN cc_start: 0.8416 (t0) cc_final: 0.8163 (t0) outliers start: 31 outliers final: 27 residues processed: 141 average time/residue: 0.0559 time to fit residues: 10.4343 Evaluate side-chains 145 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 chunk 51 optimal weight: 0.6980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.153577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132626 restraints weight = 6379.714| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.63 r_work: 0.3327 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5378 Z= 0.153 Angle : 0.578 8.553 7361 Z= 0.307 Chirality : 0.046 0.148 848 Planarity : 0.004 0.049 945 Dihedral : 5.112 24.021 752 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.25 % Allowed : 21.36 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.06 (0.32), residues: 688 helix: -0.84 (1.57), residues: 8 sheet: 0.28 (0.29), residues: 287 loop : -0.18 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 98 TYR 0.012 0.002 TYR I 148 PHE 0.015 0.002 PHE A 209 TRP 0.012 0.002 TRP M 163 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5372) covalent geometry : angle 0.57778 ( 7349) SS BOND : bond 0.00535 ( 6) SS BOND : angle 0.58608 ( 12) hydrogen bonds : bond 0.02835 ( 183) hydrogen bonds : angle 5.86723 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7469 (m-40) cc_final: 0.7112 (m-40) REVERT: A 162 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: I 2 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7404 (mt0) REVERT: I 60 ASN cc_start: 0.8430 (t0) cc_final: 0.8166 (t0) outliers start: 31 outliers final: 28 residues processed: 142 average time/residue: 0.0606 time to fit residues: 11.4409 Evaluate side-chains 150 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain I residue 2 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 123 SER Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 172 THR Chi-restraints excluded: chain M residue 176 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.153410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.132426 restraints weight = 6351.568| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.63 r_work: 0.3339 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5378 Z= 0.150 Angle : 0.575 8.419 7361 Z= 0.305 Chirality : 0.046 0.147 848 Planarity : 0.004 0.048 945 Dihedral : 5.118 23.714 752 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.42 % Allowed : 21.19 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.05 (0.32), residues: 688 helix: -0.70 (1.62), residues: 8 sheet: 0.31 (0.29), residues: 287 loop : -0.20 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 98 TYR 0.018 0.002 TYR A 175 PHE 0.015 0.002 PHE A 209 TRP 0.013 0.002 TRP M 163 HIS 0.003 0.001 HIS A 45 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5372) covalent geometry : angle 0.57456 ( 7349) SS BOND : bond 0.00537 ( 6) SS BOND : angle 0.56170 ( 12) hydrogen bonds : bond 0.02817 ( 183) hydrogen bonds : angle 5.86113 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.41 seconds wall clock time: 25 minutes 57.39 seconds (1557.39 seconds total)