Starting phenix.real_space_refine on Tue Feb 3 22:02:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.map" model { file = "/net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hkq_52234/02_2026/9hkq_52234.cif" } resolution = 3.3 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= 0.001 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 29 5.16 5 C 4569 2.51 5 N 1243 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7256 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1682 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 209} Chain: "E" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1593 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 820 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2229 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 261} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Time building chain proxies: 1.19, per 1000 atoms: 0.16 Number of scatterers: 7256 At special positions: 0 Unit cell: (66.96, 91.14, 153.45, 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 29 16.00 O 1415 8.00 N 1243 7.00 C 4569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.04 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: 0.58 Conformation dependent library (CDL) restraints added in 191.3 milliseconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 12.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'D' and resid 63 through 66 removed outlier: 3.524A pdb=" N LYS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 210 through 213 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 182 through 187 Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.627A pdb=" N ILE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 85 removed outlier: 3.589A pdb=" N GLY B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.516A pdb=" N GLN B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.743A pdb=" N THR F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.957A pdb=" N MET D 34 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR D 54 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 36 " --> pdb=" O HIS D 52 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS D 52 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP D 38 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.388A pdb=" N TYR D 111 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N TYR D 101 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE D 109 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 129 through 132 removed outlier: 3.543A pdb=" N LYS D 152 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR D 185 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 144 through 146 Processing sheet with id=AA6, first strand: chain 'D' and resid 161 through 163 removed outlier: 4.241A pdb=" N TYR D 203 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 216 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS D 209 " --> pdb=" O THR D 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 6 removed outlier: 5.442A pdb=" N THR E 68 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N SER E 27 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N SER E 66 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N VAL E 29 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 11.329A pdb=" N SER E 64 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.334A pdb=" N MET E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP E 34 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.334A pdb=" N MET E 11 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR E 96 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 113 through 117 removed outlier: 5.970A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 153 through 154 removed outlier: 4.187A pdb=" N TRP E 147 " --> pdb=" O GLN E 154 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 144 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 11 removed outlier: 5.249A pdb=" N PHE C 62 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C 55 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.721A pdb=" N GLY B 26 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 35 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 24 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP B 37 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 22 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 111 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS B 114 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 125 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 116 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 186 through 193 removed outlier: 5.570A pdb=" N PHE B 241 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 193 removed outlier: 5.570A pdb=" N PHE B 241 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 214 through 219 Processing sheet with id=AB9, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.501A pdb=" N VAL F 92 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET F 34 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALA F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.727A pdb=" N TYR F 102 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 17 through 22 removed outlier: 3.941A pdb=" N LEU F 18 " --> pdb=" O MET F 82 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 816 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: 1.00 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2341 1.34 - 1.46: 1904 1.46 - 1.58: 3159 1.58 - 1.70: 0 1.70 - 1.81: 41 Bond restraints: 7445 Sorted by residual: bond pdb=" CA ILE B 213 " pdb=" CB ILE B 213 " ideal model delta sigma weight residual 1.553 1.541 0.012 7.40e-03 1.83e+04 2.45e+00 bond pdb=" C GLU D 157 " pdb=" N PRO D 158 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.15e+00 bond pdb=" N PRO B 250 " pdb=" CA PRO B 250 " ideal model delta sigma weight residual 1.469 1.476 -0.007 7.40e-03 1.83e+04 8.99e-01 bond pdb=" CA GLN C 89 " pdb=" CB GLN C 89 " ideal model delta sigma weight residual 1.536 1.525 0.011 1.23e-02 6.61e+03 8.06e-01 bond pdb=" CA GLN C 89 " pdb=" C GLN C 89 " ideal model delta sigma weight residual 1.519 1.528 -0.009 1.01e-02 9.80e+03 7.43e-01 ... (remaining 7440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 9813 1.41 - 2.81: 242 2.81 - 4.22: 45 4.22 - 5.62: 10 5.62 - 7.03: 4 Bond angle restraints: 10114 Sorted by residual: angle pdb=" C PRO D 156 " pdb=" N GLU D 157 " pdb=" CA GLU D 157 " ideal model delta sigma weight residual 120.09 125.16 -5.07 1.25e+00 6.40e-01 1.64e+01 angle pdb=" CA TYR E 48 " pdb=" CB TYR E 48 " pdb=" CG TYR E 48 " ideal model delta sigma weight residual 113.90 119.93 -6.03 1.80e+00 3.09e-01 1.12e+01 angle pdb=" C TYR E 139 " pdb=" CA TYR E 139 " pdb=" CB TYR E 139 " ideal model delta sigma weight residual 113.57 109.32 4.25 1.57e+00 4.06e-01 7.33e+00 angle pdb=" C SER E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.25e+00 angle pdb=" CA TYR E 93 " pdb=" CB TYR E 93 " pdb=" CG TYR E 93 " ideal model delta sigma weight residual 113.90 109.11 4.79 1.80e+00 3.09e-01 7.09e+00 ... (remaining 10109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3829 17.53 - 35.06: 432 35.06 - 52.59: 103 52.59 - 70.12: 19 70.12 - 87.64: 11 Dihedral angle restraints: 4394 sinusoidal: 1712 harmonic: 2682 Sorted by residual: dihedral pdb=" CB CYS B 203 " pdb=" SG CYS B 203 " pdb=" SG CYS B 259 " pdb=" CB CYS B 259 " ideal model delta sinusoidal sigma weight residual 93.00 49.94 43.06 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 87 " pdb=" CB CYS E 87 " ideal model delta sinusoidal sigma weight residual 93.00 58.17 34.83 1 1.00e+01 1.00e-02 1.72e+01 dihedral pdb=" CA LYS B 186 " pdb=" C LYS B 186 " pdb=" N THR B 187 " pdb=" CA THR B 187 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 4391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 748 0.035 - 0.070: 232 0.070 - 0.106: 71 0.106 - 0.141: 33 0.141 - 0.176: 3 Chirality restraints: 1087 Sorted by residual: chirality pdb=" CA TYR E 93 " pdb=" N TYR E 93 " pdb=" C TYR E 93 " pdb=" CB TYR E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA TYR E 48 " pdb=" N TYR E 48 " pdb=" C TYR E 48 " pdb=" CB TYR E 48 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE E 47 " pdb=" N ILE E 47 " pdb=" C ILE E 47 " pdb=" CB ILE E 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1084 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 86 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO F 87 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 87 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 87 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 93 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.60e+00 pdb=" N PRO E 94 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 94 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 94 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 62 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO D 63 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 63 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 63 " -0.022 5.00e-02 4.00e+02 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1225 2.77 - 3.30: 6777 3.30 - 3.84: 12438 3.84 - 4.37: 15140 4.37 - 4.90: 26427 Nonbonded interactions: 62007 Sorted by model distance: nonbonded pdb=" OH TYR B 59 " pdb=" OH TYR B 171 " model vdw 2.238 3.040 nonbonded pdb=" O SER E 170 " pdb=" OG SER E 170 " model vdw 2.248 3.040 nonbonded pdb=" NH1 ARG E 60 " pdb=" OD1 ASP E 81 " model vdw 2.257 3.120 nonbonded pdb=" O TRP D 49 " pdb=" ND2 ASN D 62 " model vdw 2.269 3.120 nonbonded pdb=" OD2 ASP C 53 " pdb=" NE2 GLN B 32 " model vdw 2.273 3.120 ... (remaining 62002 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: 1.770 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.030 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 0.036 7451 Z= 0.129 Angle : 0.572 7.028 10126 Z= 0.311 Chirality : 0.042 0.176 1087 Planarity : 0.004 0.055 1295 Dihedral : 16.085 87.644 2664 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.25 % Allowed : 18.03 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.41 (0.28), residues: 912 helix: 0.88 (0.58), residues: 79 sheet: -0.21 (0.26), residues: 373 loop : -0.42 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 157 TYR 0.018 0.001 TYR E 48 PHE 0.007 0.001 PHE C 30 TRP 0.012 0.001 TRP B 60 HIS 0.004 0.001 HIS E 197 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7445) covalent geometry : angle 0.57167 (10114) SS BOND : bond 0.00234 ( 6) SS BOND : angle 0.48189 ( 12) hydrogen bonds : bond 0.21097 ( 293) hydrogen bonds : angle 9.35404 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 ASN cc_start: 0.7248 (m-40) cc_final: 0.6995 (m-40) REVERT: B 156 LEU cc_start: 0.7479 (tp) cc_final: 0.7228 (tp) REVERT: A 4 MET cc_start: 0.8001 (tpp) cc_final: 0.7575 (tpp) outliers start: 2 outliers final: 1 residues processed: 212 average time/residue: 0.0808 time to fit residues: 22.2836 Evaluate side-chains 163 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068849 restraints weight = 14175.412| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.30 r_work: 0.2822 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7451 Z= 0.173 Angle : 0.615 5.681 10126 Z= 0.329 Chirality : 0.044 0.203 1087 Planarity : 0.005 0.055 1295 Dihedral : 4.906 24.938 1013 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.40 % Allowed : 19.55 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.34 (0.28), residues: 912 helix: 0.78 (0.57), residues: 83 sheet: -0.16 (0.26), residues: 389 loop : -0.36 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 17 TYR 0.024 0.002 TYR E 93 PHE 0.012 0.001 PHE B 33 TRP 0.014 0.001 TRP B 204 HIS 0.003 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7445) covalent geometry : angle 0.61403 (10114) SS BOND : bond 0.00333 ( 6) SS BOND : angle 0.97496 ( 12) hydrogen bonds : bond 0.03740 ( 293) hydrogen bonds : angle 6.16319 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9093 (mm) REVERT: D 74 ASP cc_start: 0.8879 (t0) cc_final: 0.8533 (t0) REVERT: D 131 PHE cc_start: 0.8510 (m-80) cc_final: 0.8158 (m-10) REVERT: D 157 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8221 (tm-30) REVERT: D 208 ASN cc_start: 0.8580 (t0) cc_final: 0.8237 (t0) REVERT: E 77 MET cc_start: 0.8572 (ttt) cc_final: 0.8341 (ttt) REVERT: E 80 GLU cc_start: 0.8899 (pt0) cc_final: 0.8637 (pt0) REVERT: E 144 LYS cc_start: 0.9108 (pptt) cc_final: 0.8825 (pptt) REVERT: E 157 ASN cc_start: 0.8645 (t0) cc_final: 0.8139 (t0) REVERT: E 160 GLU cc_start: 0.8836 (tt0) cc_final: 0.8348 (tt0) REVERT: E 166 ASP cc_start: 0.8693 (t0) cc_final: 0.8382 (t0) REVERT: E 169 ASP cc_start: 0.9019 (p0) cc_final: 0.8704 (p0) REVERT: C 36 GLU cc_start: 0.7545 (mp0) cc_final: 0.7200 (mp0) REVERT: C 91 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8524 (tttp) REVERT: C 96 ASP cc_start: 0.8535 (t0) cc_final: 0.8197 (t0) REVERT: B 61 ASP cc_start: 0.9177 (m-30) cc_final: 0.8638 (m-30) REVERT: B 127 LYS cc_start: 0.7940 (mttp) cc_final: 0.7677 (mttp) REVERT: A 4 MET cc_start: 0.9053 (tpp) cc_final: 0.8237 (tpp) REVERT: F 52 ASP cc_start: 0.8898 (m-30) cc_final: 0.8632 (m-30) REVERT: F 59 TYR cc_start: 0.8302 (m-80) cc_final: 0.7974 (m-80) outliers start: 27 outliers final: 11 residues processed: 186 average time/residue: 0.0790 time to fit residues: 19.5437 Evaluate side-chains 168 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN B 32 GLN B 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.093304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069299 restraints weight = 14056.824| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.27 r_work: 0.2808 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7451 Z= 0.181 Angle : 0.599 6.504 10126 Z= 0.316 Chirality : 0.044 0.211 1087 Planarity : 0.004 0.055 1295 Dihedral : 4.746 18.742 1012 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.16 % Allowed : 19.29 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.26 (0.29), residues: 912 helix: 1.00 (0.58), residues: 82 sheet: -0.13 (0.26), residues: 395 loop : -0.32 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.025 0.002 TYR E 93 PHE 0.009 0.001 PHE B 208 TRP 0.015 0.001 TRP B 204 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7445) covalent geometry : angle 0.59793 (10114) SS BOND : bond 0.00356 ( 6) SS BOND : angle 1.05674 ( 12) hydrogen bonds : bond 0.03239 ( 293) hydrogen bonds : angle 5.59890 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9149 (mm) REVERT: D 74 ASP cc_start: 0.8865 (t0) cc_final: 0.8536 (t0) REVERT: D 131 PHE cc_start: 0.8520 (m-80) cc_final: 0.8153 (m-10) REVERT: D 157 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 208 ASN cc_start: 0.8639 (t0) cc_final: 0.8234 (t0) REVERT: E 144 LYS cc_start: 0.9130 (pptt) cc_final: 0.8800 (pptt) REVERT: E 154 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7490 (tm-30) REVERT: E 157 ASN cc_start: 0.8831 (t0) cc_final: 0.8298 (t0) REVERT: E 160 GLU cc_start: 0.8814 (tt0) cc_final: 0.8305 (tt0) REVERT: E 166 ASP cc_start: 0.8696 (t0) cc_final: 0.8428 (t0) REVERT: C 50 GLU cc_start: 0.8467 (pm20) cc_final: 0.8069 (pm20) REVERT: C 77 GLU cc_start: 0.8454 (pp20) cc_final: 0.8237 (pp20) REVERT: C 96 ASP cc_start: 0.8640 (t0) cc_final: 0.8194 (t0) REVERT: B 58 GLU cc_start: 0.9038 (pm20) cc_final: 0.8770 (pm20) REVERT: B 61 ASP cc_start: 0.9212 (m-30) cc_final: 0.8629 (m-30) REVERT: B 273 ARG cc_start: 0.8909 (mtp85) cc_final: 0.8282 (mmt180) REVERT: A 5 TRP cc_start: 0.8213 (t60) cc_final: 0.7802 (t60) REVERT: F 52 ASP cc_start: 0.8919 (m-30) cc_final: 0.8608 (m-30) REVERT: F 80 LEU cc_start: 0.9304 (tp) cc_final: 0.8914 (tt) REVERT: F 82 MET cc_start: 0.8917 (mtp) cc_final: 0.8492 (mtp) REVERT: F 94 TYR cc_start: 0.8528 (m-80) cc_final: 0.8276 (m-80) REVERT: F 99 TYR cc_start: 0.8818 (t80) cc_final: 0.8461 (t80) outliers start: 33 outliers final: 18 residues processed: 192 average time/residue: 0.0703 time to fit residues: 18.2698 Evaluate side-chains 179 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 11 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.091274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.067381 restraints weight = 14286.471| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.27 r_work: 0.2769 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 7451 Z= 0.254 Angle : 0.627 6.102 10126 Z= 0.330 Chirality : 0.045 0.240 1087 Planarity : 0.004 0.056 1295 Dihedral : 4.839 18.888 1012 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.67 % Allowed : 19.17 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.34 (0.29), residues: 912 helix: 1.08 (0.58), residues: 82 sheet: -0.25 (0.26), residues: 392 loop : -0.31 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 19 TYR 0.030 0.002 TYR E 93 PHE 0.013 0.001 PHE B 208 TRP 0.014 0.001 TRP B 204 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 7445) covalent geometry : angle 0.62597 (10114) SS BOND : bond 0.00288 ( 6) SS BOND : angle 1.17031 ( 12) hydrogen bonds : bond 0.03220 ( 293) hydrogen bonds : angle 5.51222 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.181 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: D 69 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9242 (mm) REVERT: D 74 ASP cc_start: 0.8884 (t0) cc_final: 0.8510 (t0) REVERT: D 131 PHE cc_start: 0.8540 (m-80) cc_final: 0.8164 (m-10) REVERT: D 204 ILE cc_start: 0.9084 (pt) cc_final: 0.8754 (mm) REVERT: D 208 ASN cc_start: 0.8725 (t0) cc_final: 0.8332 (t0) REVERT: E 46 TRP cc_start: 0.9099 (OUTLIER) cc_final: 0.6957 (m-90) REVERT: E 77 MET cc_start: 0.8698 (ttt) cc_final: 0.8490 (ttt) REVERT: E 150 ASP cc_start: 0.8021 (m-30) cc_final: 0.7693 (m-30) REVERT: E 157 ASN cc_start: 0.8873 (t0) cc_final: 0.8304 (t0) REVERT: E 166 ASP cc_start: 0.8782 (t0) cc_final: 0.8529 (t0) REVERT: E 177 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9327 (t) REVERT: C 50 GLU cc_start: 0.8581 (pm20) cc_final: 0.8087 (pm20) REVERT: C 67 TYR cc_start: 0.8929 (p90) cc_final: 0.8376 (p90) REVERT: C 77 GLU cc_start: 0.8410 (pp20) cc_final: 0.8096 (pp20) REVERT: C 96 ASP cc_start: 0.8797 (t0) cc_final: 0.8303 (t0) REVERT: B 58 GLU cc_start: 0.9035 (pm20) cc_final: 0.8821 (pm20) REVERT: B 61 ASP cc_start: 0.9221 (m-30) cc_final: 0.8587 (m-30) REVERT: B 127 LYS cc_start: 0.8149 (mttp) cc_final: 0.7906 (mttp) REVERT: B 186 LYS cc_start: 0.8260 (tttm) cc_final: 0.7711 (tttm) REVERT: A 5 TRP cc_start: 0.8344 (t60) cc_final: 0.7889 (t60) REVERT: F 52 ASP cc_start: 0.8910 (m-30) cc_final: 0.8592 (m-30) REVERT: F 80 LEU cc_start: 0.9274 (tp) cc_final: 0.8876 (tt) REVERT: F 99 TYR cc_start: 0.8849 (t80) cc_final: 0.8515 (t80) outliers start: 37 outliers final: 25 residues processed: 190 average time/residue: 0.0676 time to fit residues: 17.3542 Evaluate side-chains 184 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 GLN A 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.067647 restraints weight = 14351.548| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.37 r_work: 0.2780 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 7451 Z= 0.211 Angle : 0.609 5.968 10126 Z= 0.320 Chirality : 0.044 0.232 1087 Planarity : 0.004 0.054 1295 Dihedral : 4.787 18.645 1012 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.67 % Allowed : 20.68 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.32 (0.29), residues: 912 helix: 1.12 (0.58), residues: 82 sheet: -0.24 (0.26), residues: 384 loop : -0.31 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.027 0.002 TYR E 93 PHE 0.011 0.001 PHE B 208 TRP 0.017 0.001 TRP B 274 HIS 0.004 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 7445) covalent geometry : angle 0.60781 (10114) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.12871 ( 12) hydrogen bonds : bond 0.02983 ( 293) hydrogen bonds : angle 5.39263 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9266 (mm) REVERT: D 74 ASP cc_start: 0.8880 (t0) cc_final: 0.8510 (t0) REVERT: D 131 PHE cc_start: 0.8567 (m-80) cc_final: 0.8195 (m-10) REVERT: D 204 ILE cc_start: 0.9111 (pt) cc_final: 0.8804 (mm) REVERT: D 208 ASN cc_start: 0.8742 (t0) cc_final: 0.8329 (t0) REVERT: E 46 TRP cc_start: 0.9087 (OUTLIER) cc_final: 0.7126 (m-90) REVERT: E 150 ASP cc_start: 0.8058 (m-30) cc_final: 0.6934 (m-30) REVERT: E 157 ASN cc_start: 0.8948 (t0) cc_final: 0.8338 (t0) REVERT: E 166 ASP cc_start: 0.8840 (t0) cc_final: 0.8575 (t0) REVERT: C 50 GLU cc_start: 0.8556 (pm20) cc_final: 0.8230 (pm20) REVERT: C 77 GLU cc_start: 0.8440 (pp20) cc_final: 0.8146 (pp20) REVERT: C 96 ASP cc_start: 0.8847 (t0) cc_final: 0.8362 (t0) REVERT: B 61 ASP cc_start: 0.9229 (m-30) cc_final: 0.8617 (m-30) REVERT: B 127 LYS cc_start: 0.8116 (mttp) cc_final: 0.7844 (mttp) REVERT: B 273 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8010 (tpt90) REVERT: A 5 TRP cc_start: 0.8365 (t60) cc_final: 0.8008 (t60) REVERT: F 43 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8770 (mmtm) REVERT: F 52 ASP cc_start: 0.8863 (m-30) cc_final: 0.8600 (m-30) REVERT: F 80 LEU cc_start: 0.9295 (tp) cc_final: 0.8912 (tt) REVERT: F 99 TYR cc_start: 0.8851 (t80) cc_final: 0.8638 (t80) outliers start: 37 outliers final: 27 residues processed: 184 average time/residue: 0.0730 time to fit residues: 18.0845 Evaluate side-chains 181 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN E 33 HIS ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.091924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067429 restraints weight = 14411.095| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.36 r_work: 0.2778 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 7451 Z= 0.207 Angle : 0.605 5.909 10126 Z= 0.320 Chirality : 0.044 0.228 1087 Planarity : 0.004 0.056 1295 Dihedral : 4.800 19.031 1012 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.67 % Allowed : 21.31 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.28), residues: 912 helix: 1.20 (0.58), residues: 82 sheet: -0.32 (0.26), residues: 391 loop : -0.30 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 19 TYR 0.027 0.002 TYR E 93 PHE 0.010 0.001 PHE B 208 TRP 0.016 0.001 TRP B 204 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 7445) covalent geometry : angle 0.60410 (10114) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.02150 ( 12) hydrogen bonds : bond 0.02922 ( 293) hydrogen bonds : angle 5.33428 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9282 (mm) REVERT: D 74 ASP cc_start: 0.8881 (t0) cc_final: 0.8491 (t0) REVERT: D 131 PHE cc_start: 0.8581 (m-80) cc_final: 0.8202 (m-10) REVERT: D 208 ASN cc_start: 0.8729 (t0) cc_final: 0.8114 (t0) REVERT: E 46 TRP cc_start: 0.9079 (OUTLIER) cc_final: 0.7188 (m-90) REVERT: E 150 ASP cc_start: 0.8079 (m-30) cc_final: 0.6939 (m-30) REVERT: E 154 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 157 ASN cc_start: 0.9005 (t0) cc_final: 0.8379 (t0) REVERT: E 166 ASP cc_start: 0.8846 (t0) cc_final: 0.8595 (t0) REVERT: C 50 GLU cc_start: 0.8575 (pm20) cc_final: 0.8303 (pm20) REVERT: C 77 GLU cc_start: 0.8426 (pp20) cc_final: 0.8095 (pp20) REVERT: C 96 ASP cc_start: 0.8843 (t0) cc_final: 0.8320 (t0) REVERT: B 58 GLU cc_start: 0.9021 (pm20) cc_final: 0.8654 (pm20) REVERT: B 61 ASP cc_start: 0.9244 (m-30) cc_final: 0.8679 (m-30) REVERT: B 127 LYS cc_start: 0.8169 (mttp) cc_final: 0.7877 (mttp) REVERT: B 273 ARG cc_start: 0.8732 (mtp85) cc_final: 0.8200 (mmt180) REVERT: A 4 MET cc_start: 0.8469 (tpp) cc_final: 0.8015 (tpp) REVERT: A 5 TRP cc_start: 0.8401 (t60) cc_final: 0.7930 (t60) REVERT: F 52 ASP cc_start: 0.8876 (m-30) cc_final: 0.8590 (m-30) REVERT: F 80 LEU cc_start: 0.9304 (tp) cc_final: 0.8922 (tt) REVERT: F 99 TYR cc_start: 0.8835 (t80) cc_final: 0.8353 (t80) outliers start: 37 outliers final: 27 residues processed: 182 average time/residue: 0.0726 time to fit residues: 17.9653 Evaluate side-chains 180 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN E 165 GLN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067989 restraints weight = 14584.853| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.44 r_work: 0.2780 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7451 Z= 0.147 Angle : 0.599 6.983 10126 Z= 0.315 Chirality : 0.043 0.205 1087 Planarity : 0.004 0.055 1295 Dihedral : 4.691 19.081 1012 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.40 % Allowed : 22.32 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.22 (0.28), residues: 912 helix: 1.26 (0.58), residues: 82 sheet: -0.14 (0.26), residues: 383 loop : -0.29 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 19 TYR 0.024 0.001 TYR E 93 PHE 0.007 0.001 PHE B 22 TRP 0.019 0.001 TRP B 204 HIS 0.003 0.001 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7445) covalent geometry : angle 0.59883 (10114) SS BOND : bond 0.00338 ( 6) SS BOND : angle 0.96085 ( 12) hydrogen bonds : bond 0.02731 ( 293) hydrogen bonds : angle 5.16043 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9288 (mm) REVERT: D 74 ASP cc_start: 0.8863 (t0) cc_final: 0.8530 (t0) REVERT: D 131 PHE cc_start: 0.8607 (m-80) cc_final: 0.8225 (m-10) REVERT: D 208 ASN cc_start: 0.8690 (t0) cc_final: 0.8285 (t0) REVERT: E 46 TRP cc_start: 0.9047 (OUTLIER) cc_final: 0.7154 (m-90) REVERT: E 150 ASP cc_start: 0.8057 (m-30) cc_final: 0.7780 (m-30) REVERT: E 154 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7330 (tm-30) REVERT: E 157 ASN cc_start: 0.9072 (t0) cc_final: 0.8498 (t0) REVERT: E 166 ASP cc_start: 0.8801 (t0) cc_final: 0.8511 (t0) REVERT: C 50 GLU cc_start: 0.8570 (pm20) cc_final: 0.8322 (pm20) REVERT: C 77 GLU cc_start: 0.8409 (pp20) cc_final: 0.8110 (pp20) REVERT: C 96 ASP cc_start: 0.8837 (t0) cc_final: 0.8318 (t0) REVERT: B 58 GLU cc_start: 0.8995 (pm20) cc_final: 0.8620 (pm20) REVERT: B 61 ASP cc_start: 0.9230 (m-30) cc_final: 0.8650 (m-30) REVERT: B 127 LYS cc_start: 0.8226 (mttp) cc_final: 0.7930 (mttp) REVERT: B 264 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 273 ARG cc_start: 0.8639 (mtp85) cc_final: 0.8228 (mmt180) REVERT: A 5 TRP cc_start: 0.8288 (t60) cc_final: 0.7914 (t60) REVERT: F 52 ASP cc_start: 0.8826 (m-30) cc_final: 0.8559 (m-30) REVERT: F 80 LEU cc_start: 0.9338 (tp) cc_final: 0.8921 (tt) REVERT: F 82 MET cc_start: 0.8804 (mtp) cc_final: 0.8497 (mtp) REVERT: F 99 TYR cc_start: 0.8800 (t80) cc_final: 0.8335 (t80) outliers start: 27 outliers final: 23 residues processed: 180 average time/residue: 0.0698 time to fit residues: 16.9572 Evaluate side-chains 181 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.0030 chunk 66 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068206 restraints weight = 14658.236| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.36 r_work: 0.2809 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7451 Z= 0.174 Angle : 0.619 9.441 10126 Z= 0.323 Chirality : 0.044 0.212 1087 Planarity : 0.004 0.057 1295 Dihedral : 4.705 19.729 1012 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.53 % Allowed : 21.94 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.28), residues: 912 helix: 1.34 (0.57), residues: 82 sheet: -0.17 (0.26), residues: 388 loop : -0.26 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.025 0.002 TYR E 93 PHE 0.008 0.001 PHE B 208 TRP 0.016 0.001 TRP B 204 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 7445) covalent geometry : angle 0.61867 (10114) SS BOND : bond 0.00327 ( 6) SS BOND : angle 0.96642 ( 12) hydrogen bonds : bond 0.02768 ( 293) hydrogen bonds : angle 5.18268 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9294 (mm) REVERT: D 74 ASP cc_start: 0.8867 (t0) cc_final: 0.8503 (t0) REVERT: D 131 PHE cc_start: 0.8602 (m-80) cc_final: 0.8224 (m-10) REVERT: D 208 ASN cc_start: 0.8688 (t0) cc_final: 0.8300 (t0) REVERT: E 46 TRP cc_start: 0.9052 (OUTLIER) cc_final: 0.7218 (m-90) REVERT: E 144 LYS cc_start: 0.9152 (pptt) cc_final: 0.8866 (pptt) REVERT: E 154 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7246 (tm-30) REVERT: E 157 ASN cc_start: 0.9072 (t0) cc_final: 0.8513 (t0) REVERT: E 166 ASP cc_start: 0.8766 (t0) cc_final: 0.8510 (t0) REVERT: C 36 GLU cc_start: 0.7732 (mp0) cc_final: 0.7528 (mp0) REVERT: C 50 GLU cc_start: 0.8446 (pm20) cc_final: 0.8156 (pm20) REVERT: C 77 GLU cc_start: 0.8410 (pp20) cc_final: 0.8097 (pp20) REVERT: C 96 ASP cc_start: 0.8810 (t0) cc_final: 0.8250 (t0) REVERT: B 58 GLU cc_start: 0.9003 (pm20) cc_final: 0.8744 (pm20) REVERT: B 61 ASP cc_start: 0.9258 (m-30) cc_final: 0.8672 (m-30) REVERT: B 264 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8178 (mt-10) REVERT: B 273 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8217 (mmt180) REVERT: F 52 ASP cc_start: 0.8806 (m-30) cc_final: 0.8556 (m-30) REVERT: F 80 LEU cc_start: 0.9334 (tp) cc_final: 0.8925 (tt) REVERT: F 82 MET cc_start: 0.8799 (mtp) cc_final: 0.8541 (mtp) REVERT: F 99 TYR cc_start: 0.8711 (t80) cc_final: 0.8418 (t80) outliers start: 28 outliers final: 25 residues processed: 184 average time/residue: 0.0801 time to fit residues: 19.9636 Evaluate side-chains 188 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN ** E 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.067582 restraints weight = 14448.297| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.39 r_work: 0.2794 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 7451 Z= 0.194 Angle : 0.625 9.264 10126 Z= 0.324 Chirality : 0.044 0.221 1087 Planarity : 0.004 0.056 1295 Dihedral : 4.768 20.138 1012 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.91 % Allowed : 22.07 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.29), residues: 912 helix: 1.35 (0.57), residues: 82 sheet: -0.24 (0.26), residues: 391 loop : -0.18 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.026 0.002 TYR E 93 PHE 0.009 0.001 PHE B 208 TRP 0.015 0.001 TRP B 204 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 7445) covalent geometry : angle 0.62438 (10114) SS BOND : bond 0.00321 ( 6) SS BOND : angle 0.97295 ( 12) hydrogen bonds : bond 0.02772 ( 293) hydrogen bonds : angle 5.20309 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9317 (mm) REVERT: D 74 ASP cc_start: 0.8884 (t0) cc_final: 0.8521 (t0) REVERT: D 131 PHE cc_start: 0.8612 (m-80) cc_final: 0.8235 (m-10) REVERT: D 208 ASN cc_start: 0.8726 (t0) cc_final: 0.8342 (t0) REVERT: E 46 TRP cc_start: 0.9094 (OUTLIER) cc_final: 0.7210 (m-90) REVERT: E 144 LYS cc_start: 0.9172 (pptt) cc_final: 0.8890 (pptt) REVERT: E 150 ASP cc_start: 0.8116 (m-30) cc_final: 0.7013 (m-30) REVERT: E 154 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7217 (tm-30) REVERT: E 157 ASN cc_start: 0.9066 (t0) cc_final: 0.8500 (t0) REVERT: E 160 GLU cc_start: 0.8776 (tt0) cc_final: 0.8455 (tp30) REVERT: E 166 ASP cc_start: 0.8800 (t0) cc_final: 0.8536 (t0) REVERT: C 36 GLU cc_start: 0.7770 (mp0) cc_final: 0.7556 (mp0) REVERT: C 50 GLU cc_start: 0.8429 (pm20) cc_final: 0.8101 (pm20) REVERT: C 77 GLU cc_start: 0.8414 (pp20) cc_final: 0.8106 (pp20) REVERT: C 96 ASP cc_start: 0.8882 (t0) cc_final: 0.8318 (t0) REVERT: B 61 ASP cc_start: 0.9245 (m-30) cc_final: 0.8668 (m-30) REVERT: B 264 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8195 (mt-10) REVERT: B 273 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8088 (mmt180) REVERT: F 29 SER cc_start: 0.7492 (m) cc_final: 0.7047 (p) REVERT: F 52 ASP cc_start: 0.8814 (m-30) cc_final: 0.8543 (m-30) REVERT: F 80 LEU cc_start: 0.9327 (tp) cc_final: 0.9047 (tt) REVERT: F 99 TYR cc_start: 0.8856 (t80) cc_final: 0.8612 (t80) outliers start: 31 outliers final: 26 residues processed: 183 average time/residue: 0.0834 time to fit residues: 20.6917 Evaluate side-chains 186 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN E 198 GLN A 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068723 restraints weight = 14468.774| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.43 r_work: 0.2791 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7451 Z= 0.147 Angle : 0.619 9.181 10126 Z= 0.321 Chirality : 0.043 0.200 1087 Planarity : 0.004 0.056 1295 Dihedral : 4.682 21.199 1012 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.90 % Allowed : 22.95 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.10 (0.29), residues: 912 helix: 1.32 (0.57), residues: 82 sheet: -0.11 (0.26), residues: 390 loop : -0.15 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 19 TYR 0.024 0.001 TYR E 93 PHE 0.008 0.001 PHE B 22 TRP 0.018 0.001 TRP B 204 HIS 0.002 0.001 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7445) covalent geometry : angle 0.61886 (10114) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.91124 ( 12) hydrogen bonds : bond 0.02681 ( 293) hydrogen bonds : angle 5.09317 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ASP cc_start: 0.8841 (t0) cc_final: 0.8504 (t0) REVERT: D 131 PHE cc_start: 0.8613 (m-80) cc_final: 0.8228 (m-10) REVERT: D 208 ASN cc_start: 0.8697 (t0) cc_final: 0.8324 (t0) REVERT: E 46 TRP cc_start: 0.9051 (OUTLIER) cc_final: 0.7140 (m-90) REVERT: E 144 LYS cc_start: 0.9151 (pptt) cc_final: 0.8877 (pptt) REVERT: E 154 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7176 (tm-30) REVERT: E 157 ASN cc_start: 0.9053 (t0) cc_final: 0.8472 (t0) REVERT: E 160 GLU cc_start: 0.8799 (tt0) cc_final: 0.8525 (tp30) REVERT: E 166 ASP cc_start: 0.8747 (t0) cc_final: 0.8479 (t0) REVERT: E 194 GLU cc_start: 0.8348 (pm20) cc_final: 0.8041 (pm20) REVERT: C 36 GLU cc_start: 0.7757 (mp0) cc_final: 0.7529 (mp0) REVERT: C 50 GLU cc_start: 0.8390 (pm20) cc_final: 0.8055 (pm20) REVERT: C 67 TYR cc_start: 0.8896 (p90) cc_final: 0.8655 (p90) REVERT: C 77 GLU cc_start: 0.8369 (pp20) cc_final: 0.8061 (pp20) REVERT: C 96 ASP cc_start: 0.8846 (t0) cc_final: 0.8254 (t0) REVERT: B 61 ASP cc_start: 0.9243 (m-30) cc_final: 0.8639 (m-30) REVERT: B 264 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 273 ARG cc_start: 0.8522 (mtp85) cc_final: 0.8145 (mmt180) REVERT: F 29 SER cc_start: 0.7428 (m) cc_final: 0.6876 (p) REVERT: F 52 ASP cc_start: 0.8817 (m-30) cc_final: 0.8535 (m-30) outliers start: 23 outliers final: 20 residues processed: 177 average time/residue: 0.0848 time to fit residues: 20.3138 Evaluate side-chains 174 residues out of total 793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 122 GLU Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain F residue 34 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 95 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 213 ASN A 8 GLN F 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068007 restraints weight = 14456.879| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.42 r_work: 0.2807 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7451 Z= 0.187 Angle : 0.634 9.319 10126 Z= 0.329 Chirality : 0.044 0.216 1087 Planarity : 0.004 0.056 1295 Dihedral : 4.758 20.643 1012 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.53 % Allowed : 22.45 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.08 (0.29), residues: 912 helix: 1.32 (0.57), residues: 82 sheet: -0.02 (0.26), residues: 381 loop : -0.22 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.026 0.002 TYR E 93 PHE 0.009 0.001 PHE B 208 TRP 0.018 0.001 TRP A 5 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7445) covalent geometry : angle 0.63313 (10114) SS BOND : bond 0.00321 ( 6) SS BOND : angle 0.95024 ( 12) hydrogen bonds : bond 0.02758 ( 293) hydrogen bonds : angle 5.13144 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.43 seconds wall clock time: 26 minutes 51.32 seconds (1611.32 seconds total)