Starting phenix.real_space_refine on Tue Feb 3 17:51:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9log_63248/02_2026/9log_63248.map" } resolution = 3.5 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= 0.003 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 39 5.16 5 C 3645 2.51 5 N 974 2.21 5 O 1161 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 5819 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2444 Classifications: {'peptide': 318} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "B" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1668 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "C" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1607 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 199} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.31, per 1000 atoms: 0.23 Number of scatterers: 5819 At special positions: 0 Unit cell: (73.916, 143.484, 71.742, 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 39 16.00 O 1161 8.00 N 974 7.00 C 3645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 49 " distance=2.04 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 156 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 327 " distance=2.02 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 303 " distance=2.04 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 280 " distance=2.03 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 198 " 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 Links applied ALPHA1-3 " MAN E 3 " - " MAN E 6 " " MAN E 4 " - " MAN E 5 " ALPHA1-4 " NAG E 2 " - " MAN E 3 " ALPHA1-6 " MAN E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG D 1 " - " ASN A 33 " " NAG E 1 " - " ASN A 63 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 340.7 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 18 sheets defined 15.0% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.755A pdb=" N LYS A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.853A pdb=" N SER A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.506A pdb=" N ARG A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 160 through 163 removed outlier: 4.095A pdb=" N SER A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.680A pdb=" N PHE A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.172A pdb=" N VAL A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 4.152A pdb=" N ARG B 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.927A pdb=" N THR B 91 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'C' and resid 126 through 132 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.805A pdb=" N HIS C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 removed outlier: 5.916A pdb=" N LEU A 167 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.783A pdb=" N SER A 81 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 129 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 175 " --> pdb=" O PHE A 129 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU A 131 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180 removed outlier: 4.086A pdb=" N ALA A 228 " --> pdb=" O MET A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.702A pdb=" N ILE A 208 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 259 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.742A pdb=" N LYS B 12 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 33 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 51 " --> pdb=" O PHE B 34 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 134 through 138 removed outlier: 5.493A pdb=" N ALA B 151 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 198 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY B 153 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 196 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 155 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 194 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS B 157 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B 192 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 146 removed outlier: 5.493A pdb=" N ALA B 151 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 198 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY B 153 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 196 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 155 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N SER B 194 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS B 157 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU B 192 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.500A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 9 through 10 Processing sheet with id=AB6, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 119 through 123 removed outlier: 5.794A pdb=" N TYR C 177 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 119 through 123 removed outlier: 5.794A pdb=" N TYR C 177 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 160 removed outlier: 4.287A pdb=" N TRP C 153 " --> pdb=" O VAL C 160 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1849 1.34 - 1.47: 1532 1.47 - 1.59: 2530 1.59 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 5963 Sorted by residual: bond pdb=" CB TRP A 60 " pdb=" CG TRP A 60 " ideal model delta sigma weight residual 1.498 1.421 0.077 3.10e-02 1.04e+03 6.11e+00 bond pdb=" C LYS B 12 " pdb=" N LYS B 13 " ideal model delta sigma weight residual 1.327 1.362 -0.036 1.71e-02 3.42e+03 4.32e+00 bond pdb=" CB TRP A 174 " pdb=" CG TRP A 174 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.40e+00 bond pdb=" C1 MAN E 5 " pdb=" C2 MAN E 5 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.370 0.036 2.00e-02 2.50e+03 3.26e+00 ... (remaining 5958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 7811 2.29 - 4.59: 240 4.59 - 6.88: 35 6.88 - 9.18: 6 9.18 - 11.47: 2 Bond angle restraints: 8094 Sorted by residual: angle pdb=" N ARG A 74 " pdb=" CA ARG A 74 " pdb=" C ARG A 74 " ideal model delta sigma weight residual 111.92 121.14 -9.22 1.34e+00 5.57e-01 4.74e+01 angle pdb=" N GLU A 261 " pdb=" CA GLU A 261 " pdb=" C GLU A 261 " ideal model delta sigma weight residual 108.52 116.51 -7.99 1.74e+00 3.30e-01 2.11e+01 angle pdb=" C GLY C 52 " pdb=" N ASN C 53 " pdb=" CA ASN C 53 " ideal model delta sigma weight residual 121.54 129.37 -7.83 1.91e+00 2.74e-01 1.68e+01 angle pdb=" N MET A 337 " pdb=" CA MET A 337 " pdb=" C MET A 337 " ideal model delta sigma weight residual 110.17 105.17 5.00 1.51e+00 4.39e-01 1.10e+01 angle pdb=" CA LEU C 20 " pdb=" CB LEU C 20 " pdb=" CG LEU C 20 " ideal model delta sigma weight residual 116.30 127.77 -11.47 3.50e+00 8.16e-02 1.07e+01 ... (remaining 8089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3281 17.71 - 35.41: 279 35.41 - 53.12: 83 53.12 - 70.82: 22 70.82 - 88.53: 10 Dihedral angle restraints: 3675 sinusoidal: 1519 harmonic: 2156 Sorted by residual: dihedral pdb=" CA ASP B 111 " pdb=" C ASP B 111 " pdb=" N TYR B 112 " pdb=" CA TYR B 112 " ideal model delta harmonic sigma weight residual -180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA SER A 65 " pdb=" C SER A 65 " pdb=" N GLN A 66 " pdb=" CA GLN A 66 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR A 276 " pdb=" C THR A 276 " pdb=" N SER A 277 " pdb=" CA SER A 277 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 3672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 897 0.260 - 0.519: 3 0.519 - 0.779: 0 0.779 - 1.038: 0 1.038 - 1.298: 1 Chirality restraints: 901 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 63 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA ARG A 74 " pdb=" N ARG A 74 " pdb=" C ARG A 74 " pdb=" CB ARG A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C4 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" C5 NAG E 2 " pdb=" O4 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 898 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 97 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 98 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 167 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 168 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 56 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 57 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " -0.031 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 735 2.75 - 3.28: 5130 3.28 - 3.82: 9818 3.82 - 4.36: 10998 4.36 - 4.90: 19208 Nonbonded interactions: 45889 Sorted by model distance: nonbonded pdb=" O VAL C 110 " pdb=" OH TYR C 145 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 159 " pdb=" OE1 GLU B 162 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLU A 201 " pdb=" OH TYR A 318 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP B 90 " pdb=" OH TYR B 94 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 93 " pdb=" OG SER A 93 " model vdw 2.281 3.040 ... (remaining 45884 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.490 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 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 : 0.008 0.077 5983 Z= 0.355 Angle : 1.032 19.104 8142 Z= 0.533 Chirality : 0.071 1.298 901 Planarity : 0.009 0.074 1031 Dihedral : 15.920 88.526 2271 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 10.41 % Allowed : 10.09 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.27), residues: 752 helix: -2.67 (0.39), residues: 88 sheet: -0.82 (0.34), residues: 223 loop : -2.89 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.019 0.003 TYR A 138 PHE 0.025 0.003 PHE A 202 TRP 0.025 0.003 TRP B 36 HIS 0.008 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00772 ( 5963) covalent geometry : angle 0.96881 ( 8094) SS BOND : bond 0.00692 ( 12) SS BOND : angle 1.36977 ( 24) hydrogen bonds : bond 0.13091 ( 209) hydrogen bonds : angle 8.02163 ( 561) link_ALPHA1-3 : bond 0.00530 ( 2) link_ALPHA1-3 : angle 2.08921 ( 6) link_ALPHA1-4 : bond 0.00377 ( 1) link_ALPHA1-4 : angle 6.49334 ( 3) link_ALPHA1-6 : bond 0.00151 ( 1) link_ALPHA1-6 : angle 1.92423 ( 3) link_BETA1-4 : bond 0.01689 ( 2) link_BETA1-4 : angle 6.09765 ( 6) link_NAG-ASN : bond 0.00813 ( 2) link_NAG-ASN : angle 10.31020 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 90 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.6428 (OUTLIER) cc_final: 0.6174 (p) REVERT: A 313 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6503 (mm-30) REVERT: B 83 LEU cc_start: 0.8062 (tp) cc_final: 0.7741 (tp) REVERT: B 192 LEU cc_start: 0.0998 (OUTLIER) cc_final: 0.0704 (pp) REVERT: C 77 ILE cc_start: 0.3673 (OUTLIER) cc_final: 0.3282 (mt) outliers start: 66 outliers final: 33 residues processed: 146 average time/residue: 0.0766 time to fit residues: 14.4121 Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 87 ASN A 199 GLN A 309 HIS B 39 GLN B 178 HIS C 1 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.181293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141062 restraints weight = 11462.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.143914 restraints weight = 6431.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.144781 restraints weight = 4119.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.145612 restraints weight = 3165.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.145715 restraints weight = 2617.342| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5983 Z= 0.141 Angle : 0.734 19.141 8142 Z= 0.356 Chirality : 0.053 0.752 901 Planarity : 0.006 0.057 1031 Dihedral : 10.705 67.149 1031 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.84 % Allowed : 13.72 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.29), residues: 752 helix: -1.53 (0.49), residues: 89 sheet: -0.28 (0.36), residues: 223 loop : -2.46 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 91 TYR 0.021 0.001 TYR A 138 PHE 0.017 0.002 PHE C 144 TRP 0.015 0.001 TRP A 141 HIS 0.008 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5963) covalent geometry : angle 0.67321 ( 8094) SS BOND : bond 0.00433 ( 12) SS BOND : angle 0.80162 ( 24) hydrogen bonds : bond 0.03797 ( 209) hydrogen bonds : angle 6.80494 ( 561) link_ALPHA1-3 : bond 0.00639 ( 2) link_ALPHA1-3 : angle 1.65521 ( 6) link_ALPHA1-4 : bond 0.00056 ( 1) link_ALPHA1-4 : angle 4.22091 ( 3) link_ALPHA1-6 : bond 0.00384 ( 1) link_ALPHA1-6 : angle 1.44175 ( 3) link_BETA1-4 : bond 0.00468 ( 2) link_BETA1-4 : angle 3.84945 ( 6) link_NAG-ASN : bond 0.01228 ( 2) link_NAG-ASN : angle 9.44024 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 VAL cc_start: 0.6919 (OUTLIER) cc_final: 0.6678 (p) REVERT: A 255 ASP cc_start: 0.7561 (t70) cc_final: 0.7010 (m-30) REVERT: A 310 LYS cc_start: 0.8789 (pttt) cc_final: 0.8006 (pttt) REVERT: A 313 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: B 36 TRP cc_start: 0.7270 (m100) cc_final: 0.6939 (m-90) REVERT: B 71 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7607 (p) REVERT: B 83 LEU cc_start: 0.7754 (tp) cc_final: 0.7500 (tp) outliers start: 37 outliers final: 20 residues processed: 107 average time/residue: 0.0665 time to fit residues: 9.6477 Evaluate side-chains 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain C residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.140611 restraints weight = 11123.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143528 restraints weight = 5803.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.145306 restraints weight = 3862.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.146421 restraints weight = 3047.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.147091 restraints weight = 2634.235| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5983 Z= 0.143 Angle : 0.676 11.337 8142 Z= 0.331 Chirality : 0.048 0.380 901 Planarity : 0.006 0.053 1031 Dihedral : 8.983 59.657 1001 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.21 % Allowed : 15.46 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.30), residues: 752 helix: -0.61 (0.55), residues: 88 sheet: -0.07 (0.36), residues: 228 loop : -2.18 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.024 0.001 TYR A 83 PHE 0.014 0.001 PHE A 330 TRP 0.012 0.001 TRP A 141 HIS 0.005 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5963) covalent geometry : angle 0.63599 ( 8094) SS BOND : bond 0.00352 ( 12) SS BOND : angle 0.68169 ( 24) hydrogen bonds : bond 0.03536 ( 209) hydrogen bonds : angle 6.30970 ( 561) link_ALPHA1-3 : bond 0.00743 ( 2) link_ALPHA1-3 : angle 1.79183 ( 6) link_ALPHA1-4 : bond 0.00595 ( 1) link_ALPHA1-4 : angle 3.03960 ( 3) link_ALPHA1-6 : bond 0.00676 ( 1) link_ALPHA1-6 : angle 1.24150 ( 3) link_BETA1-4 : bond 0.00408 ( 2) link_BETA1-4 : angle 5.23734 ( 6) link_NAG-ASN : bond 0.02881 ( 2) link_NAG-ASN : angle 6.02501 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7696 (t80) cc_final: 0.7464 (t80) REVERT: A 108 VAL cc_start: 0.7057 (OUTLIER) cc_final: 0.6819 (p) REVERT: A 255 ASP cc_start: 0.7414 (t70) cc_final: 0.6899 (m-30) REVERT: A 313 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: B 23 LYS cc_start: 0.8388 (mptt) cc_final: 0.8187 (mptt) REVERT: B 67 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6705 (ttt180) REVERT: B 71 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7561 (p) REVERT: C 75 LEU cc_start: 0.7781 (tp) cc_final: 0.7463 (tp) REVERT: C 88 TYR cc_start: 0.7441 (m-80) cc_final: 0.7049 (m-80) outliers start: 33 outliers final: 20 residues processed: 98 average time/residue: 0.0592 time to fit residues: 8.0289 Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 130 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.180200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139100 restraints weight = 11312.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.142020 restraints weight = 5918.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.143912 restraints weight = 3951.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144904 restraints weight = 3085.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.145608 restraints weight = 2699.427| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5983 Z= 0.172 Angle : 0.660 8.553 8142 Z= 0.330 Chirality : 0.048 0.402 901 Planarity : 0.005 0.049 1031 Dihedral : 8.828 59.647 997 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.52 % Allowed : 17.35 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.30), residues: 752 helix: -0.54 (0.54), residues: 88 sheet: -0.06 (0.36), residues: 230 loop : -2.09 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 67 TYR 0.020 0.001 TYR A 138 PHE 0.013 0.001 PHE A 191 TRP 0.011 0.001 TRP A 141 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 5963) covalent geometry : angle 0.62776 ( 8094) SS BOND : bond 0.00379 ( 12) SS BOND : angle 0.83677 ( 24) hydrogen bonds : bond 0.03635 ( 209) hydrogen bonds : angle 6.19368 ( 561) link_ALPHA1-3 : bond 0.00417 ( 2) link_ALPHA1-3 : angle 1.53550 ( 6) link_ALPHA1-4 : bond 0.00687 ( 1) link_ALPHA1-4 : angle 4.07274 ( 3) link_ALPHA1-6 : bond 0.00491 ( 1) link_ALPHA1-6 : angle 1.50894 ( 3) link_BETA1-4 : bond 0.00414 ( 2) link_BETA1-4 : angle 4.74872 ( 6) link_NAG-ASN : bond 0.01008 ( 2) link_NAG-ASN : angle 4.65038 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7744 (t80) cc_final: 0.7482 (t80) REVERT: A 108 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6822 (p) REVERT: A 255 ASP cc_start: 0.7521 (t70) cc_final: 0.7259 (t70) REVERT: A 284 MET cc_start: 0.6302 (ppp) cc_final: 0.5926 (pmm) REVERT: B 81 MET cc_start: 0.7536 (ttp) cc_final: 0.7252 (ttm) REVERT: B 98 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.7645 (ptm160) REVERT: C 75 LEU cc_start: 0.7813 (tp) cc_final: 0.7481 (tp) REVERT: C 88 TYR cc_start: 0.7493 (m-80) cc_final: 0.7211 (m-80) outliers start: 35 outliers final: 24 residues processed: 92 average time/residue: 0.0621 time to fit residues: 7.9628 Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.175425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135969 restraints weight = 11440.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138783 restraints weight = 5886.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140510 restraints weight = 3905.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141456 restraints weight = 3079.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142086 restraints weight = 2706.261| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5983 Z= 0.269 Angle : 0.734 7.514 8142 Z= 0.374 Chirality : 0.049 0.396 901 Planarity : 0.006 0.045 1031 Dihedral : 8.966 59.752 993 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 6.31 % Allowed : 16.88 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.30), residues: 752 helix: -0.61 (0.55), residues: 88 sheet: -0.22 (0.35), residues: 237 loop : -2.14 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 324 TYR 0.021 0.002 TYR A 83 PHE 0.020 0.002 PHE A 330 TRP 0.014 0.002 TRP C 37 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 5963) covalent geometry : angle 0.70545 ( 8094) SS BOND : bond 0.00528 ( 12) SS BOND : angle 1.18361 ( 24) hydrogen bonds : bond 0.04364 ( 209) hydrogen bonds : angle 6.40981 ( 561) link_ALPHA1-3 : bond 0.00457 ( 2) link_ALPHA1-3 : angle 1.71355 ( 6) link_ALPHA1-4 : bond 0.00850 ( 1) link_ALPHA1-4 : angle 3.91459 ( 3) link_ALPHA1-6 : bond 0.00229 ( 1) link_ALPHA1-6 : angle 1.58096 ( 3) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 4.83529 ( 6) link_NAG-ASN : bond 0.00650 ( 2) link_NAG-ASN : angle 4.25407 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7834 (t80) cc_final: 0.7589 (t80) REVERT: A 108 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6799 (p) REVERT: A 255 ASP cc_start: 0.7555 (t70) cc_final: 0.7288 (t70) REVERT: C 88 TYR cc_start: 0.7599 (m-80) cc_final: 0.7268 (m-80) outliers start: 40 outliers final: 32 residues processed: 95 average time/residue: 0.0584 time to fit residues: 7.8792 Evaluate side-chains 87 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.180437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140214 restraints weight = 11147.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143560 restraints weight = 5526.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145639 restraints weight = 3545.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.146903 restraints weight = 2691.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.147461 restraints weight = 2284.292| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5983 Z= 0.123 Angle : 0.640 8.377 8142 Z= 0.318 Chirality : 0.047 0.430 901 Planarity : 0.005 0.044 1031 Dihedral : 8.364 57.044 993 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.26 % Allowed : 18.61 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.31), residues: 752 helix: -0.33 (0.56), residues: 88 sheet: -0.40 (0.34), residues: 256 loop : -1.90 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.014 0.001 TYR A 138 PHE 0.010 0.001 PHE A 130 TRP 0.013 0.001 TRP A 141 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5963) covalent geometry : angle 0.61025 ( 8094) SS BOND : bond 0.00326 ( 12) SS BOND : angle 0.84651 ( 24) hydrogen bonds : bond 0.03400 ( 209) hydrogen bonds : angle 6.10756 ( 561) link_ALPHA1-3 : bond 0.00557 ( 2) link_ALPHA1-3 : angle 1.57482 ( 6) link_ALPHA1-4 : bond 0.00831 ( 1) link_ALPHA1-4 : angle 3.58022 ( 3) link_ALPHA1-6 : bond 0.00345 ( 1) link_ALPHA1-6 : angle 1.31187 ( 3) link_BETA1-4 : bond 0.00445 ( 2) link_BETA1-4 : angle 4.31180 ( 6) link_NAG-ASN : bond 0.00997 ( 2) link_NAG-ASN : angle 4.67117 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8262 (pp) REVERT: A 83 TYR cc_start: 0.7648 (t80) cc_final: 0.7360 (t80) REVERT: A 255 ASP cc_start: 0.7580 (t70) cc_final: 0.7222 (t70) REVERT: A 284 MET cc_start: 0.6501 (ppp) cc_final: 0.5937 (pmm) REVERT: A 310 LYS cc_start: 0.8434 (pptt) cc_final: 0.7922 (pptt) REVERT: B 36 TRP cc_start: 0.7245 (m100) cc_final: 0.6925 (m-90) REVERT: C 75 LEU cc_start: 0.7883 (tp) cc_final: 0.7546 (tp) REVERT: C 88 TYR cc_start: 0.7471 (m-80) cc_final: 0.7189 (m-80) outliers start: 27 outliers final: 20 residues processed: 86 average time/residue: 0.0581 time to fit residues: 6.9213 Evaluate side-chains 81 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.181423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.141355 restraints weight = 11377.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.144203 restraints weight = 5931.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.146040 restraints weight = 3953.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.146993 restraints weight = 3080.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.147635 restraints weight = 2691.908| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5983 Z= 0.130 Angle : 0.645 10.144 8142 Z= 0.317 Chirality : 0.046 0.421 901 Planarity : 0.005 0.062 1031 Dihedral : 8.060 54.851 991 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.57 % Allowed : 19.09 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.31), residues: 752 helix: -0.35 (0.57), residues: 88 sheet: -0.07 (0.35), residues: 237 loop : -1.89 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.012 0.001 TYR A 138 PHE 0.033 0.002 PHE C 144 TRP 0.011 0.001 TRP A 141 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5963) covalent geometry : angle 0.60683 ( 8094) SS BOND : bond 0.00335 ( 12) SS BOND : angle 2.28001 ( 24) hydrogen bonds : bond 0.03335 ( 209) hydrogen bonds : angle 6.08189 ( 561) link_ALPHA1-3 : bond 0.00490 ( 2) link_ALPHA1-3 : angle 1.54011 ( 6) link_ALPHA1-4 : bond 0.00729 ( 1) link_ALPHA1-4 : angle 3.38718 ( 3) link_ALPHA1-6 : bond 0.00481 ( 1) link_ALPHA1-6 : angle 1.48079 ( 3) link_BETA1-4 : bond 0.00473 ( 2) link_BETA1-4 : angle 4.22365 ( 6) link_NAG-ASN : bond 0.00927 ( 2) link_NAG-ASN : angle 4.54198 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 83 TYR cc_start: 0.7713 (t80) cc_final: 0.7450 (t80) REVERT: A 284 MET cc_start: 0.6349 (ppp) cc_final: 0.5834 (pmm) REVERT: B 48 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6565 (mtm) REVERT: B 98 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7852 (ptm-80) REVERT: C 75 LEU cc_start: 0.7787 (tp) cc_final: 0.7452 (tp) REVERT: C 88 TYR cc_start: 0.7436 (m-80) cc_final: 0.7129 (m-80) outliers start: 29 outliers final: 22 residues processed: 85 average time/residue: 0.0666 time to fit residues: 7.9390 Evaluate side-chains 83 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 GLN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.183732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.142911 restraints weight = 11128.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146024 restraints weight = 5647.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.148019 restraints weight = 3700.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.149214 restraints weight = 2839.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149811 restraints weight = 2422.783| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5983 Z= 0.117 Angle : 0.626 8.126 8142 Z= 0.308 Chirality : 0.046 0.428 901 Planarity : 0.005 0.056 1031 Dihedral : 7.742 58.750 990 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.94 % Allowed : 20.03 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.31), residues: 752 helix: -0.29 (0.56), residues: 91 sheet: -0.04 (0.34), residues: 254 loop : -1.74 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.028 0.001 TYR A 138 PHE 0.031 0.002 PHE C 144 TRP 0.011 0.001 TRP A 141 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5963) covalent geometry : angle 0.59479 ( 8094) SS BOND : bond 0.00330 ( 12) SS BOND : angle 1.36241 ( 24) hydrogen bonds : bond 0.03158 ( 209) hydrogen bonds : angle 5.88890 ( 561) link_ALPHA1-3 : bond 0.00476 ( 2) link_ALPHA1-3 : angle 1.48364 ( 6) link_ALPHA1-4 : bond 0.00802 ( 1) link_ALPHA1-4 : angle 3.17675 ( 3) link_ALPHA1-6 : bond 0.00442 ( 1) link_ALPHA1-6 : angle 1.43129 ( 3) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 4.11293 ( 6) link_NAG-ASN : bond 0.00979 ( 2) link_NAG-ASN : angle 4.62126 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 83 TYR cc_start: 0.7691 (t80) cc_final: 0.7442 (t80) REVERT: A 284 MET cc_start: 0.6212 (ppp) cc_final: 0.5564 (pmm) REVERT: B 48 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6550 (mtm) REVERT: B 98 ARG cc_start: 0.8117 (ttp-170) cc_final: 0.7799 (ptm-80) REVERT: C 32 ASP cc_start: 0.7600 (t70) cc_final: 0.7344 (t70) REVERT: C 51 TYR cc_start: 0.6288 (p90) cc_final: 0.5998 (p90) outliers start: 25 outliers final: 20 residues processed: 83 average time/residue: 0.0731 time to fit residues: 8.2050 Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.177377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137864 restraints weight = 11388.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140824 restraints weight = 5914.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.142609 restraints weight = 3901.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.143815 restraints weight = 3017.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144428 restraints weight = 2542.602| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5983 Z= 0.233 Angle : 0.689 7.261 8142 Z= 0.346 Chirality : 0.048 0.377 901 Planarity : 0.006 0.050 1031 Dihedral : 7.928 57.271 988 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.57 % Allowed : 19.24 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.31), residues: 752 helix: -0.27 (0.57), residues: 88 sheet: 0.04 (0.36), residues: 232 loop : -1.83 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.016 0.002 TYR A 138 PHE 0.035 0.003 PHE A 225 TRP 0.019 0.002 TRP A 247 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 5963) covalent geometry : angle 0.65932 ( 8094) SS BOND : bond 0.00471 ( 12) SS BOND : angle 1.60362 ( 24) hydrogen bonds : bond 0.03940 ( 209) hydrogen bonds : angle 6.16178 ( 561) link_ALPHA1-3 : bond 0.00642 ( 2) link_ALPHA1-3 : angle 1.63692 ( 6) link_ALPHA1-4 : bond 0.00783 ( 1) link_ALPHA1-4 : angle 3.27849 ( 3) link_ALPHA1-6 : bond 0.00228 ( 1) link_ALPHA1-6 : angle 1.63445 ( 3) link_BETA1-4 : bond 0.00416 ( 2) link_BETA1-4 : angle 4.48042 ( 6) link_NAG-ASN : bond 0.00632 ( 2) link_NAG-ASN : angle 4.17494 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8270 (pp) REVERT: A 83 TYR cc_start: 0.7824 (t80) cc_final: 0.7486 (t80) REVERT: A 284 MET cc_start: 0.6302 (ppp) cc_final: 0.5700 (pmm) REVERT: A 310 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8165 (pptt) REVERT: B 48 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6535 (mtm) REVERT: B 98 ARG cc_start: 0.8133 (ttp-170) cc_final: 0.7869 (ptm-80) REVERT: C 32 ASP cc_start: 0.7684 (t70) cc_final: 0.7466 (t70) REVERT: C 88 TYR cc_start: 0.7580 (m-80) cc_final: 0.7280 (m-80) outliers start: 29 outliers final: 21 residues processed: 82 average time/residue: 0.0739 time to fit residues: 8.2105 Evaluate side-chains 81 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.181496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.140970 restraints weight = 11360.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.143845 restraints weight = 5866.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.145735 restraints weight = 3873.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146882 restraints weight = 3025.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.147665 restraints weight = 2610.592| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5983 Z= 0.124 Angle : 0.644 8.214 8142 Z= 0.317 Chirality : 0.047 0.409 901 Planarity : 0.005 0.054 1031 Dihedral : 7.579 59.116 988 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.79 % Allowed : 19.56 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.31), residues: 752 helix: -0.11 (0.57), residues: 88 sheet: -0.14 (0.35), residues: 246 loop : -1.64 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.020 0.001 TYR A 138 PHE 0.029 0.002 PHE C 144 TRP 0.018 0.001 TRP A 247 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5963) covalent geometry : angle 0.61461 ( 8094) SS BOND : bond 0.00345 ( 12) SS BOND : angle 1.14312 ( 24) hydrogen bonds : bond 0.03215 ( 209) hydrogen bonds : angle 6.02721 ( 561) link_ALPHA1-3 : bond 0.00572 ( 2) link_ALPHA1-3 : angle 1.47364 ( 6) link_ALPHA1-4 : bond 0.00807 ( 1) link_ALPHA1-4 : angle 3.02872 ( 3) link_ALPHA1-6 : bond 0.00387 ( 1) link_ALPHA1-6 : angle 1.41855 ( 3) link_BETA1-4 : bond 0.00530 ( 2) link_BETA1-4 : angle 4.22068 ( 6) link_NAG-ASN : bond 0.00854 ( 2) link_NAG-ASN : angle 4.66410 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8243 (pp) REVERT: A 83 TYR cc_start: 0.7747 (t80) cc_final: 0.7418 (t80) REVERT: A 247 TRP cc_start: 0.7213 (m100) cc_final: 0.6816 (m100) REVERT: A 284 MET cc_start: 0.6349 (ppp) cc_final: 0.5659 (pmm) REVERT: B 48 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6526 (mtm) REVERT: B 98 ARG cc_start: 0.8100 (ttp-170) cc_final: 0.7830 (ptm-80) REVERT: C 32 ASP cc_start: 0.7626 (t70) cc_final: 0.7370 (t70) REVERT: C 88 TYR cc_start: 0.7466 (m-80) cc_final: 0.7198 (m-80) outliers start: 24 outliers final: 20 residues processed: 78 average time/residue: 0.0659 time to fit residues: 7.1539 Evaluate side-chains 84 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.177820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.137593 restraints weight = 11294.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140335 restraints weight = 5897.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.142138 restraints weight = 3945.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.143104 restraints weight = 3091.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.143750 restraints weight = 2701.700| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5983 Z= 0.205 Angle : 0.682 7.601 8142 Z= 0.341 Chirality : 0.048 0.374 901 Planarity : 0.006 0.050 1031 Dihedral : 7.492 57.753 986 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.26 % Allowed : 19.09 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.31), residues: 752 helix: 0.04 (0.59), residues: 82 sheet: 0.03 (0.36), residues: 232 loop : -1.70 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.015 0.002 TYR A 138 PHE 0.025 0.002 PHE A 225 TRP 0.023 0.002 TRP A 247 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5963) covalent geometry : angle 0.65402 ( 8094) SS BOND : bond 0.00433 ( 12) SS BOND : angle 1.40327 ( 24) hydrogen bonds : bond 0.03723 ( 209) hydrogen bonds : angle 6.15762 ( 561) link_ALPHA1-3 : bond 0.00510 ( 2) link_ALPHA1-3 : angle 1.57066 ( 6) link_ALPHA1-4 : bond 0.00882 ( 1) link_ALPHA1-4 : angle 3.08620 ( 3) link_ALPHA1-6 : bond 0.00255 ( 1) link_ALPHA1-6 : angle 1.58947 ( 3) link_BETA1-4 : bond 0.00442 ( 2) link_BETA1-4 : angle 4.38312 ( 6) link_NAG-ASN : bond 0.00666 ( 2) link_NAG-ASN : angle 4.20325 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1184.14 seconds wall clock time: 21 minutes 9.84 seconds (1269.84 seconds total)