Starting phenix.real_space_refine on Wed Feb 4 00:28:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.map" model { file = "/net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jzq_61939/02_2026/9jzq_61939.cif" } resolution = 3.48 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= 0.005 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 32 5.16 5 C 4968 2.51 5 N 1327 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 7890 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1255 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 8, 'TRANS': 147} Chain: "A" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1707 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208} Chain: "B" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1605 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 196} Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1684 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 210} Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 1.78, per 1000 atoms: 0.23 Number of scatterers: 7890 At special positions: 0 Unit cell: (69, 122.82, 185.61, 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 32 16.00 O 1563 8.00 N 1327 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 220 " - pdb=" SG CYS E 226 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 203 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 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: 0.74 Conformation dependent library (CDL) restraints added in 232.1 milliseconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 24 sheets defined 6.4% alpha, 46.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.626A pdb=" N ALA E 212 " --> pdb=" O THR E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 269 through 274 removed outlier: 3.723A pdb=" N GLU E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 269 through 274' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.666A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 removed outlier: 4.024A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 172 through 175 removed outlier: 3.620A pdb=" N ILE E 172 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 316 " --> pdb=" O ILE E 172 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 174 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR E 318 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE E 300 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 246 " --> pdb=" O TRP E 200 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N PHE E 202 " --> pdb=" O GLN E 244 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN E 244 " --> pdb=" O PHE E 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 182 through 185 Processing sheet with id=AA3, first strand: chain 'E' and resid 215 through 220 Processing sheet with id=AA4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.700A pdb=" N VAL A 36 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 52 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP A 38 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.968A pdb=" N TYR A 109 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER A 101 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE A 107 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.615A pdb=" N ASP A 151 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR A 183 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.699A pdb=" N TYR A 201 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 12 removed outlier: 7.070A pdb=" N TRP B 34 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 46 " --> pdb=" O TRP B 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.701A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 3.701A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 155 through 156 Processing sheet with id=AB6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.708A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 50 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C 59 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.148A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 139 through 140 removed outlier: 3.563A pdb=" N THR C 143 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR C 184 " --> pdb=" O ASP C 152 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 185 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 177 " --> pdb=" O SER C 185 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 162 removed outlier: 4.385A pdb=" N TYR C 202 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.582A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 33 " --> pdb=" O ASN D 49 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.502A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.416A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 193 " --> pdb=" O LYS D 149 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 864 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: 1.10 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2538 1.35 - 1.47: 1975 1.47 - 1.59: 3529 1.59 - 1.71: 0 1.71 - 1.83: 40 Bond restraints: 8082 Sorted by residual: bond pdb=" CA GLY D 64 " pdb=" C GLY D 64 " ideal model delta sigma weight residual 1.520 1.511 0.009 7.30e-03 1.88e+04 1.42e+00 bond pdb=" C MET C 40 " pdb=" O MET C 40 " ideal model delta sigma weight residual 1.236 1.249 -0.013 1.27e-02 6.20e+03 1.03e+00 bond pdb=" CA VAL A 191 " pdb=" CB VAL A 191 " ideal model delta sigma weight residual 1.547 1.537 0.010 1.10e-02 8.26e+03 8.45e-01 bond pdb=" CB PRO D 95 " pdb=" CG PRO D 95 " ideal model delta sigma weight residual 1.506 1.541 -0.035 3.90e-02 6.57e+02 7.84e-01 bond pdb=" CB ASN E 302 " pdb=" CG ASN E 302 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.62e-01 ... (remaining 8077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10853 2.05 - 4.09: 153 4.09 - 6.14: 13 6.14 - 8.18: 1 8.18 - 10.23: 3 Bond angle restraints: 11023 Sorted by residual: angle pdb=" N GLN C 67 " pdb=" CA GLN C 67 " pdb=" C GLN C 67 " ideal model delta sigma weight residual 114.04 110.24 3.80 1.24e+00 6.50e-01 9.41e+00 angle pdb=" C GLY D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.76e+00 angle pdb=" CA LEU B 134 " pdb=" CB LEU B 134 " pdb=" CG LEU B 134 " ideal model delta sigma weight residual 116.30 126.53 -10.23 3.50e+00 8.16e-02 8.54e+00 angle pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sigma weight residual 116.30 126.51 -10.21 3.50e+00 8.16e-02 8.50e+00 angle pdb=" CB MET A 87 " pdb=" CG MET A 87 " pdb=" SD MET A 87 " ideal model delta sigma weight residual 112.70 120.91 -8.21 3.00e+00 1.11e-01 7.48e+00 ... (remaining 11018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4167 17.82 - 35.64: 526 35.64 - 53.46: 126 53.46 - 71.27: 22 71.27 - 89.09: 16 Dihedral angle restraints: 4857 sinusoidal: 1877 harmonic: 2980 Sorted by residual: dihedral pdb=" CB CYS C 224 " pdb=" SG CYS C 224 " pdb=" SG CYS D 214 " pdb=" CB CYS D 214 " ideal model delta sinusoidal sigma weight residual -86.00 -168.45 82.45 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 223 " pdb=" SG CYS A 223 " pdb=" SG CYS B 213 " pdb=" CB CYS B 213 " ideal model delta sinusoidal sigma weight residual 93.00 168.54 -75.54 1 1.00e+01 1.00e-02 7.20e+01 dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 203 " pdb=" CB CYS A 203 " ideal model delta sinusoidal sigma weight residual 93.00 40.04 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 4854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 877 0.037 - 0.074: 234 0.074 - 0.111: 116 0.111 - 0.148: 25 0.148 - 0.185: 1 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CA PRO D 95 " pdb=" N PRO D 95 " pdb=" C PRO D 95 " pdb=" CB PRO D 95 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA PRO B 8 " pdb=" N PRO B 8 " pdb=" C PRO B 8 " pdb=" CB PRO B 8 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL C 37 " pdb=" N VAL C 37 " pdb=" C VAL C 37 " pdb=" CB VAL C 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 1250 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 52 " -0.050 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO C 53 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 61 " 0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO C 62 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 94 " -0.050 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO D 95 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.037 5.00e-02 4.00e+02 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 221 2.69 - 3.25: 6910 3.25 - 3.80: 11585 3.80 - 4.35: 14657 4.35 - 4.90: 25392 Nonbonded interactions: 58765 Sorted by model distance: nonbonded pdb=" OG1 THR D 63 " pdb=" OG1 THR D 74 " model vdw 2.142 3.040 nonbonded pdb=" NZ LYS B 165 " pdb=" O PRO B 166 " model vdw 2.209 3.120 nonbonded pdb=" OE1 GLN D 166 " pdb=" OH TYR D 173 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG A 68 " pdb=" O ASN A 86 " model vdw 2.270 3.120 nonbonded pdb=" O HIS D 189 " pdb=" NH2 ARG D 211 " model vdw 2.273 3.120 ... (remaining 58760 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: 4.310 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.003 0.035 8094 Z= 0.120 Angle : 0.594 10.226 11047 Z= 0.306 Chirality : 0.043 0.185 1253 Planarity : 0.006 0.077 1412 Dihedral : 16.907 89.092 2907 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.45 % Allowed : 30.46 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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 (0.27), residues: 1023 helix: -0.01 (0.84), residues: 37 sheet: 1.16 (0.25), residues: 478 loop : -0.50 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.017 0.001 TYR C 153 PHE 0.019 0.001 PHE B 141 TRP 0.045 0.002 TRP A 55 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8082) covalent geometry : angle 0.59332 (11023) SS BOND : bond 0.00342 ( 12) SS BOND : angle 0.79875 ( 24) hydrogen bonds : bond 0.10154 ( 308) hydrogen bonds : angle 6.31547 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.248 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: A 151 ASP cc_start: 0.5849 (m-30) cc_final: 0.4913 (m-30) REVERT: C 43 ARG cc_start: 0.8041 (ptm160) cc_final: 0.7396 (ptm160) outliers start: 4 outliers final: 1 residues processed: 168 average time/residue: 0.1190 time to fit residues: 25.0694 Evaluate side-chains 89 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN B 190 HIS C 99 HIS D 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.099027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.064486 restraints weight = 34549.876| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 7.58 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8094 Z= 0.302 Angle : 0.739 10.457 11047 Z= 0.375 Chirality : 0.046 0.169 1253 Planarity : 0.006 0.080 1412 Dihedral : 5.270 63.499 1104 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 7.05 % Allowed : 24.86 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.30 (0.27), residues: 1023 helix: 0.29 (0.86), residues: 37 sheet: 1.03 (0.24), residues: 489 loop : -0.66 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 195 TYR 0.015 0.002 TYR A 152 PHE 0.018 0.002 PHE B 141 TRP 0.015 0.002 TRP A 55 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 8082) covalent geometry : angle 0.73756 (11023) SS BOND : bond 0.00442 ( 12) SS BOND : angle 1.26027 ( 24) hydrogen bonds : bond 0.04118 ( 308) hydrogen bonds : angle 5.80219 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 83 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 191 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8533 (pt) REVERT: E 287 LYS cc_start: 0.8721 (tttm) cc_final: 0.8410 (ttpt) REVERT: A 34 MET cc_start: 0.8851 (mmm) cc_final: 0.8441 (mmm) REVERT: A 69 LEU cc_start: 0.8681 (mt) cc_final: 0.8452 (mp) REVERT: A 151 ASP cc_start: 0.8688 (m-30) cc_final: 0.8324 (m-30) REVERT: A 170 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.6126 (m) REVERT: B 105 LEU cc_start: 0.9164 (tp) cc_final: 0.8750 (tp) REVERT: B 142 TYR cc_start: 0.8598 (t80) cc_final: 0.8204 (t80) REVERT: C 93 MET cc_start: 0.8234 (tpp) cc_final: 0.7988 (tpt) REVERT: C 101 ARG cc_start: 0.9219 (mtt-85) cc_final: 0.9009 (mtt-85) REVERT: C 152 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8536 (p0) REVERT: D 103 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8796 (ptmm) outliers start: 63 outliers final: 36 residues processed: 134 average time/residue: 0.0854 time to fit residues: 15.9886 Evaluate side-chains 109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 69 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 255 LYS Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 50.0000 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.112887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.088074 restraints weight = 38151.590| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 5.76 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8094 Z= 0.158 Angle : 0.628 10.472 11047 Z= 0.318 Chirality : 0.044 0.146 1253 Planarity : 0.005 0.068 1412 Dihedral : 5.039 62.051 1103 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.26 % Allowed : 26.65 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.36 (0.27), residues: 1023 helix: 0.12 (0.80), residues: 38 sheet: 1.09 (0.24), residues: 483 loop : -0.59 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 211 TYR 0.013 0.001 TYR A 152 PHE 0.019 0.001 PHE E 182 TRP 0.011 0.001 TRP D 94 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8082) covalent geometry : angle 0.62782 (11023) SS BOND : bond 0.00399 ( 12) SS BOND : angle 0.88685 ( 24) hydrogen bonds : bond 0.03312 ( 308) hydrogen bonds : angle 5.41710 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ILE cc_start: 0.9058 (pt) cc_final: 0.8832 (mt) REVERT: E 191 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8393 (pt) REVERT: E 256 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8406 (mtmt) REVERT: E 260 GLN cc_start: 0.8927 (tt0) cc_final: 0.8562 (mm-40) REVERT: E 287 LYS cc_start: 0.8727 (tttm) cc_final: 0.8406 (ttpt) REVERT: A 34 MET cc_start: 0.8774 (mmm) cc_final: 0.8363 (mmm) REVERT: A 69 LEU cc_start: 0.8821 (mt) cc_final: 0.8457 (mp) REVERT: A 91 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.6740 (t0) REVERT: A 112 GLN cc_start: 0.8963 (mp10) cc_final: 0.8749 (mp10) REVERT: A 151 ASP cc_start: 0.8257 (m-30) cc_final: 0.7613 (m-30) REVERT: B 142 TYR cc_start: 0.8473 (t80) cc_final: 0.7810 (t80) REVERT: B 193 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8343 (t80) REVERT: B 212 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: C 152 ASP cc_start: 0.9117 (OUTLIER) cc_final: 0.8515 (p0) outliers start: 47 outliers final: 27 residues processed: 117 average time/residue: 0.0815 time to fit residues: 13.6406 Evaluate side-chains 109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 256 LYS Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 40.0000 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.098324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.064040 restraints weight = 34914.262| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 7.50 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8094 Z= 0.187 Angle : 0.624 11.613 11047 Z= 0.316 Chirality : 0.044 0.160 1253 Planarity : 0.005 0.087 1412 Dihedral : 5.041 61.580 1103 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.60 % Allowed : 27.10 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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 (0.27), residues: 1023 helix: 0.33 (0.83), residues: 38 sheet: 0.94 (0.24), residues: 493 loop : -0.62 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 98 TYR 0.019 0.002 TYR D 186 PHE 0.015 0.001 PHE E 182 TRP 0.010 0.001 TRP E 262 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8082) covalent geometry : angle 0.62360 (11023) SS BOND : bond 0.00405 ( 12) SS BOND : angle 0.88568 ( 24) hydrogen bonds : bond 0.03374 ( 308) hydrogen bonds : angle 5.33648 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 80 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8867 (mt) REVERT: E 260 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.9003 (mm-40) REVERT: E 287 LYS cc_start: 0.8721 (tttm) cc_final: 0.8406 (ttpt) REVERT: A 34 MET cc_start: 0.8802 (mmm) cc_final: 0.8389 (mmm) REVERT: A 69 LEU cc_start: 0.8720 (mt) cc_final: 0.8472 (mp) REVERT: A 151 ASP cc_start: 0.8749 (m-30) cc_final: 0.8377 (m-30) REVERT: A 171 HIS cc_start: 0.8701 (t-90) cc_final: 0.8395 (t-90) REVERT: B 142 TYR cc_start: 0.8780 (t80) cc_final: 0.8029 (t80) REVERT: B 193 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8205 (t80) outliers start: 50 outliers final: 34 residues processed: 121 average time/residue: 0.0783 time to fit residues: 13.7989 Evaluate side-chains 108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.096912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062698 restraints weight = 35061.630| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 7.36 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8094 Z= 0.252 Angle : 0.664 13.390 11047 Z= 0.335 Chirality : 0.044 0.205 1253 Planarity : 0.005 0.062 1412 Dihedral : 5.165 61.635 1103 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.60 % Allowed : 26.99 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.15 (0.27), residues: 1023 helix: 0.47 (0.84), residues: 38 sheet: 0.92 (0.24), residues: 487 loop : -0.77 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 98 TYR 0.011 0.002 TYR A 152 PHE 0.017 0.001 PHE E 182 TRP 0.014 0.002 TRP E 262 HIS 0.007 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 8082) covalent geometry : angle 0.66348 (11023) SS BOND : bond 0.00412 ( 12) SS BOND : angle 0.91409 ( 24) hydrogen bonds : bond 0.03644 ( 308) hydrogen bonds : angle 5.47246 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 70 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 260 GLN cc_start: 0.9178 (tt0) cc_final: 0.8834 (mm-40) REVERT: E 268 SER cc_start: 0.7954 (p) cc_final: 0.7691 (p) REVERT: E 287 LYS cc_start: 0.8757 (tttm) cc_final: 0.8436 (ttpt) REVERT: A 34 MET cc_start: 0.8809 (mmm) cc_final: 0.8350 (mmm) REVERT: A 151 ASP cc_start: 0.8739 (m-30) cc_final: 0.8318 (m-30) REVERT: A 171 HIS cc_start: 0.8743 (t-90) cc_final: 0.8405 (t-90) REVERT: B 142 TYR cc_start: 0.8918 (t80) cc_final: 0.8286 (t80) REVERT: C 71 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8846 (p) REVERT: D 189 HIS cc_start: 0.8802 (m-70) cc_final: 0.8358 (m-70) outliers start: 50 outliers final: 44 residues processed: 110 average time/residue: 0.0738 time to fit residues: 11.9838 Evaluate side-chains 114 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 69 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.097944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.063783 restraints weight = 34829.246| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 7.60 r_work: 0.3037 rms_B_bonded: 7.55 restraints_weight: 2.0000 r_work: 0.3178 rms_B_bonded: 5.40 restraints_weight: 4.0000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8094 Z= 0.146 Angle : 0.633 14.655 11047 Z= 0.315 Chirality : 0.044 0.237 1253 Planarity : 0.005 0.052 1412 Dihedral : 4.997 60.726 1103 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.14 % Allowed : 27.77 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.28 (0.27), residues: 1023 helix: -0.02 (0.79), residues: 38 sheet: 1.02 (0.24), residues: 484 loop : -0.64 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 98 TYR 0.010 0.001 TYR A 152 PHE 0.013 0.001 PHE E 182 TRP 0.008 0.001 TRP E 262 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8082) covalent geometry : angle 0.62917 (11023) SS BOND : bond 0.00418 ( 12) SS BOND : angle 1.58389 ( 24) hydrogen bonds : bond 0.03129 ( 308) hydrogen bonds : angle 5.21010 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8406 (t) REVERT: E 243 ASP cc_start: 0.8788 (t0) cc_final: 0.8546 (t0) REVERT: E 260 GLN cc_start: 0.9247 (tt0) cc_final: 0.8881 (mm-40) REVERT: E 287 LYS cc_start: 0.8649 (tttm) cc_final: 0.8371 (ttpt) REVERT: A 34 MET cc_start: 0.8913 (mmm) cc_final: 0.8479 (mmm) REVERT: A 151 ASP cc_start: 0.8839 (m-30) cc_final: 0.8504 (m-30) REVERT: A 171 HIS cc_start: 0.8131 (t-90) cc_final: 0.7907 (t-90) REVERT: B 142 TYR cc_start: 0.8810 (t80) cc_final: 0.8197 (t80) REVERT: C 156 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8687 (mp0) REVERT: D 189 HIS cc_start: 0.8877 (m-70) cc_final: 0.8399 (m-70) outliers start: 37 outliers final: 31 residues processed: 104 average time/residue: 0.0810 time to fit residues: 12.1481 Evaluate side-chains 101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 overall best weight: 1.3144 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.111807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.086839 restraints weight = 39234.703| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.72 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8094 Z= 0.123 Angle : 0.619 15.170 11047 Z= 0.306 Chirality : 0.043 0.169 1253 Planarity : 0.005 0.085 1412 Dihedral : 4.854 59.895 1103 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.93 % Allowed : 27.44 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.38 (0.27), residues: 1023 helix: -0.02 (0.82), residues: 38 sheet: 1.04 (0.24), residues: 484 loop : -0.51 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.011 0.001 TYR B 179 PHE 0.013 0.001 PHE E 182 TRP 0.007 0.001 TRP E 262 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8082) covalent geometry : angle 0.61612 (11023) SS BOND : bond 0.00413 ( 12) SS BOND : angle 1.33036 ( 24) hydrogen bonds : bond 0.02913 ( 308) hydrogen bonds : angle 4.99924 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8414 (t) REVERT: E 243 ASP cc_start: 0.8819 (t0) cc_final: 0.8594 (t0) REVERT: E 260 GLN cc_start: 0.9007 (tt0) cc_final: 0.8604 (mm-40) REVERT: E 287 LYS cc_start: 0.8779 (tttm) cc_final: 0.8497 (ttpt) REVERT: E 296 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 34 MET cc_start: 0.8754 (mmt) cc_final: 0.8270 (mmm) REVERT: A 65 LEU cc_start: 0.9013 (tt) cc_final: 0.8782 (pt) REVERT: A 151 ASP cc_start: 0.8353 (m-30) cc_final: 0.7709 (m-30) REVERT: A 171 HIS cc_start: 0.8995 (t-90) cc_final: 0.8586 (t-90) REVERT: B 142 TYR cc_start: 0.8822 (t80) cc_final: 0.8168 (t80) REVERT: D 189 HIS cc_start: 0.8861 (m-70) cc_final: 0.8421 (m-70) outliers start: 44 outliers final: 35 residues processed: 108 average time/residue: 0.0797 time to fit residues: 12.4811 Evaluate side-chains 100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 0.0170 chunk 32 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.6022 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.098158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.064141 restraints weight = 34557.680| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 7.54 r_work: 0.3046 rms_B_bonded: 7.45 restraints_weight: 2.0000 r_work: 0.3189 rms_B_bonded: 5.39 restraints_weight: 4.0000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8094 Z= 0.136 Angle : 0.613 15.443 11047 Z= 0.303 Chirality : 0.043 0.142 1253 Planarity : 0.005 0.060 1412 Dihedral : 4.857 59.536 1103 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.59 % Allowed : 27.88 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.36 (0.27), residues: 1023 helix: 0.04 (0.83), residues: 38 sheet: 1.05 (0.24), residues: 481 loop : -0.54 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 66 TYR 0.014 0.001 TYR B 179 PHE 0.013 0.001 PHE E 182 TRP 0.008 0.001 TRP E 262 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8082) covalent geometry : angle 0.61189 (11023) SS BOND : bond 0.00312 ( 12) SS BOND : angle 0.99656 ( 24) hydrogen bonds : bond 0.02981 ( 308) hydrogen bonds : angle 5.02585 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 199 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8384 (t) REVERT: E 243 ASP cc_start: 0.8848 (t0) cc_final: 0.8592 (t0) REVERT: E 287 LYS cc_start: 0.8633 (tttm) cc_final: 0.8392 (ttpt) REVERT: E 296 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 34 MET cc_start: 0.8903 (mmt) cc_final: 0.8454 (mmm) REVERT: A 65 LEU cc_start: 0.9071 (tt) cc_final: 0.8855 (pt) REVERT: A 151 ASP cc_start: 0.8823 (m-30) cc_final: 0.8511 (m-30) REVERT: B 142 TYR cc_start: 0.8842 (t80) cc_final: 0.8217 (t80) REVERT: C 156 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8659 (mp0) REVERT: D 189 HIS cc_start: 0.8903 (m-70) cc_final: 0.8441 (m-70) outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 0.0753 time to fit residues: 11.1588 Evaluate side-chains 109 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 70 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 296 LEU Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.110494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.085576 restraints weight = 38961.347| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.66 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8094 Z= 0.168 Angle : 0.624 14.618 11047 Z= 0.310 Chirality : 0.043 0.142 1253 Planarity : 0.005 0.060 1412 Dihedral : 4.913 59.256 1103 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.38 % Allowed : 26.65 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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 (0.27), residues: 1023 helix: 0.05 (0.84), residues: 38 sheet: 0.97 (0.24), residues: 481 loop : -0.62 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 TYR 0.015 0.001 TYR B 179 PHE 0.014 0.001 PHE E 182 TRP 0.010 0.001 TRP E 262 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8082) covalent geometry : angle 0.62291 (11023) SS BOND : bond 0.00321 ( 12) SS BOND : angle 1.02242 ( 24) hydrogen bonds : bond 0.03126 ( 308) hydrogen bonds : angle 5.10248 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 76 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 243 ASP cc_start: 0.8904 (t0) cc_final: 0.8694 (t0) REVERT: E 260 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8762 (mm-40) REVERT: E 287 LYS cc_start: 0.8811 (tttm) cc_final: 0.8530 (ttpt) REVERT: A 34 MET cc_start: 0.8779 (mmt) cc_final: 0.8234 (mmm) REVERT: A 151 ASP cc_start: 0.8326 (m-30) cc_final: 0.7683 (m-30) REVERT: A 171 HIS cc_start: 0.8716 (t-90) cc_final: 0.8323 (t-90) REVERT: B 60 ARG cc_start: 0.7742 (ptp90) cc_final: 0.7300 (ptp90) REVERT: B 142 TYR cc_start: 0.8815 (t80) cc_final: 0.8148 (t80) REVERT: C 55 ASP cc_start: 0.8456 (p0) cc_final: 0.8252 (p0) REVERT: C 71 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8675 (p) REVERT: C 156 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: D 189 HIS cc_start: 0.8935 (m-70) cc_final: 0.8477 (m-70) outliers start: 48 outliers final: 42 residues processed: 117 average time/residue: 0.0809 time to fit residues: 13.3390 Evaluate side-chains 118 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 73 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 40.0000 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.062865 restraints weight = 34454.638| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 7.59 r_work: 0.3020 rms_B_bonded: 7.54 restraints_weight: 2.0000 r_work: 0.3161 rms_B_bonded: 5.41 restraints_weight: 4.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8094 Z= 0.181 Angle : 0.626 9.466 11047 Z= 0.314 Chirality : 0.044 0.170 1253 Planarity : 0.005 0.058 1412 Dihedral : 4.986 60.031 1103 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.26 % Allowed : 26.99 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.21 (0.27), residues: 1023 helix: 0.01 (0.83), residues: 38 sheet: 0.95 (0.24), residues: 479 loop : -0.64 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 45 TYR 0.014 0.001 TYR B 179 PHE 0.014 0.001 PHE E 182 TRP 0.010 0.001 TRP E 262 HIS 0.004 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8082) covalent geometry : angle 0.62448 (11023) SS BOND : bond 0.00329 ( 12) SS BOND : angle 1.05033 ( 24) hydrogen bonds : bond 0.03248 ( 308) hydrogen bonds : angle 5.14656 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 243 ASP cc_start: 0.8962 (t0) cc_final: 0.8725 (t0) REVERT: E 260 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8931 (mm-40) REVERT: E 287 LYS cc_start: 0.8675 (tttm) cc_final: 0.8409 (ttpt) REVERT: A 34 MET cc_start: 0.8938 (mmt) cc_final: 0.8440 (mmm) REVERT: A 151 ASP cc_start: 0.8818 (m-30) cc_final: 0.8526 (m-30) REVERT: B 60 ARG cc_start: 0.8090 (ptp90) cc_final: 0.7679 (ptp90) REVERT: B 142 TYR cc_start: 0.8792 (t80) cc_final: 0.8150 (t80) REVERT: C 71 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (p) REVERT: C 156 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: D 189 HIS cc_start: 0.8993 (m-70) cc_final: 0.8710 (m-70) outliers start: 47 outliers final: 39 residues processed: 112 average time/residue: 0.0616 time to fit residues: 9.9985 Evaluate side-chains 112 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 193 TYR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 205 ASN Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 94 TRP Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 201 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.0050 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.110190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.084048 restraints weight = 38943.214| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.78 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8094 Z= 0.152 Angle : 0.629 8.842 11047 Z= 0.317 Chirality : 0.044 0.140 1253 Planarity : 0.005 0.059 1412 Dihedral : 5.041 60.976 1103 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.93 % Allowed : 27.66 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % 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: 0.24 (0.27), residues: 1023 helix: 0.03 (0.83), residues: 38 sheet: 0.97 (0.24), residues: 479 loop : -0.62 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 66 TYR 0.016 0.001 TYR B 179 PHE 0.024 0.001 PHE A 173 TRP 0.009 0.001 TRP E 262 HIS 0.007 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8082) covalent geometry : angle 0.62279 (11023) SS BOND : bond 0.00329 ( 12) SS BOND : angle 2.05663 ( 24) hydrogen bonds : bond 0.03116 ( 308) hydrogen bonds : angle 5.07679 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.32 seconds wall clock time: 48 minutes 23.47 seconds (2903.47 seconds total)