Starting phenix.real_space_refine on Tue Feb 3 21:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i9j_52760/02_2026/9i9j_52760.map" } resolution = 3.1 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= 0.004 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 38 5.16 5 C 4547 2.51 5 N 1196 2.21 5 O 1267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7053 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2196 Unusual residues: {'ACE': 1} Classifications: {'peptide': 269, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 255} Chain breaks: 3 Chain: "J" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2310 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 271} Chain breaks: 2 Chain: "K" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1978 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 15, 'TRANS': 230} Chain breaks: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.70, per 1000 atoms: 0.24 Number of scatterers: 7053 At special positions: 0 Unit cell: (77.52, 98.94, 105.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 4 15.00 Mg 1 11.99 O 1267 8.00 N 1196 7.00 C 4547 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 267.3 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 55.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 263 through 268 removed outlier: 3.704A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 275 removed outlier: 3.558A pdb=" N ASN H 273 " --> pdb=" O GLY H 270 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL H 275 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 285 removed outlier: 3.546A pdb=" N GLY H 285 " --> pdb=" O GLN H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 301 removed outlier: 3.699A pdb=" N ALA H 292 " --> pdb=" O THR H 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 4 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.753A pdb=" N LEU I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 94 removed outlier: 3.700A pdb=" N VAL I 80 " --> pdb=" O PRO I 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN I 93 " --> pdb=" O ARG I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 116 removed outlier: 4.047A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 136 through 154 removed outlier: 4.612A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 Processing helix chain 'I' and resid 185 through 201 removed outlier: 4.266A pdb=" N LYS I 189 " --> pdb=" O GLU I 185 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N THR I 190 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 245 through 262 Processing helix chain 'I' and resid 266 through 284 Processing helix chain 'J' and resid 47 through 51 removed outlier: 3.689A pdb=" N ALA J 51 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 67 Processing helix chain 'J' and resid 98 through 104 Processing helix chain 'J' and resid 110 through 131 removed outlier: 3.536A pdb=" N HIS J 131 " --> pdb=" O TYR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 192 through 209 Processing helix chain 'J' and resid 217 through 230 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 265 through 276 Processing helix chain 'J' and resid 285 through 291 removed outlier: 3.551A pdb=" N LYS J 291 " --> pdb=" O THR J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 297 removed outlier: 3.788A pdb=" N SER J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'K' and resid 49 through 57 removed outlier: 3.621A pdb=" N GLU K 57 " --> pdb=" O SER K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 100 through 121 removed outlier: 3.587A pdb=" N HIS K 121 " --> pdb=" O PHE K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 175 Processing helix chain 'K' and resid 182 through 199 removed outlier: 3.826A pdb=" N ILE K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 220 Processing helix chain 'K' and resid 229 through 233 removed outlier: 3.901A pdb=" N MET K 233 " --> pdb=" O VAL K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 252 removed outlier: 3.686A pdb=" N VAL K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 267 Processing helix chain 'K' and resid 276 through 282 removed outlier: 3.601A pdb=" N ALA K 282 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 14 through 20 removed outlier: 6.931A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU J 20 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP J 79 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASP J 92 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N LEU J 77 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 14 through 20 removed outlier: 6.931A pdb=" N VAL J 26 " --> pdb=" O LEU J 18 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLU J 20 " --> pdb=" O ALA J 24 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE J 87 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'J' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'K' and resid 8 through 12 removed outlier: 5.635A pdb=" N LYS K 9 " --> pdb=" O LYS K 20 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS K 20 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP K 68 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLU K 81 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LEU K 66 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.882A pdb=" N GLN K 85 " --> pdb=" O ILE K 135 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1008 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: 0.69 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2239 1.34 - 1.46: 1436 1.46 - 1.58: 3479 1.58 - 1.69: 6 1.69 - 1.81: 60 Bond restraints: 7220 Sorted by residual: bond pdb=" C ACE I 0 " pdb=" O ACE I 0 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C4 ADP J 401 " pdb=" C5 ADP J 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C4 ADP K 301 " pdb=" C5 ADP K 301 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 9.21e-01 bond pdb=" CA MET I 237 " pdb=" CB MET I 237 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.87e-01 bond pdb=" C LEU K 101 " pdb=" N PRO K 102 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.02e-01 ... (remaining 7215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 9603 1.53 - 3.05: 126 3.05 - 4.58: 31 4.58 - 6.11: 13 6.11 - 7.64: 7 Bond angle restraints: 9780 Sorted by residual: angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CB MET I 237 " pdb=" CG MET I 237 " pdb=" SD MET I 237 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.18e+00 angle pdb=" CA LEU K 101 " pdb=" CB LEU K 101 " pdb=" CG LEU K 101 " ideal model delta sigma weight residual 116.30 123.94 -7.64 3.50e+00 8.16e-02 4.76e+00 angle pdb=" CA MET I 54 " pdb=" CB MET I 54 " pdb=" CG MET I 54 " ideal model delta sigma weight residual 114.10 118.24 -4.14 2.00e+00 2.50e-01 4.28e+00 angle pdb=" CA LEU J 151 " pdb=" CB LEU J 151 " pdb=" CG LEU J 151 " ideal model delta sigma weight residual 116.30 123.54 -7.24 3.50e+00 8.16e-02 4.27e+00 ... (remaining 9775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.71: 3954 24.71 - 49.42: 351 49.42 - 74.13: 33 74.13 - 98.84: 5 98.84 - 123.55: 1 Dihedral angle restraints: 4344 sinusoidal: 1803 harmonic: 2541 Sorted by residual: dihedral pdb=" O2A ADP K 301 " pdb=" O3A ADP K 301 " pdb=" PA ADP K 301 " pdb=" PB ADP K 301 " ideal model delta sinusoidal sigma weight residual -60.00 63.55 -123.55 1 2.00e+01 2.50e-03 3.73e+01 dihedral pdb=" CG ARG H 268 " pdb=" CD ARG H 268 " pdb=" NE ARG H 268 " pdb=" CZ ARG H 268 " ideal model delta sinusoidal sigma weight residual -90.00 -133.77 43.77 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG K 217 " pdb=" CD ARG K 217 " pdb=" NE ARG K 217 " pdb=" CZ ARG K 217 " ideal model delta sinusoidal sigma weight residual 90.00 132.97 -42.97 2 1.50e+01 4.44e-03 9.91e+00 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 699 0.029 - 0.057: 242 0.057 - 0.086: 78 0.086 - 0.115: 57 0.115 - 0.143: 9 Chirality restraints: 1085 Sorted by residual: chirality pdb=" CA VAL J 210 " pdb=" N VAL J 210 " pdb=" C VAL J 210 " pdb=" CB VAL J 210 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA LEU K 101 " pdb=" N LEU K 101 " pdb=" C LEU K 101 " pdb=" CB LEU K 101 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE K 63 " pdb=" N ILE K 63 " pdb=" C ILE K 63 " pdb=" CB ILE K 63 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1082 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG J 298 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO J 299 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 299 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 299 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 210 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO J 211 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO J 211 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 211 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET I 237 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C MET I 237 " -0.029 2.00e-02 2.50e+03 pdb=" O MET I 237 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU I 238 " 0.010 2.00e-02 2.50e+03 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 101 2.67 - 3.23: 6401 3.23 - 3.79: 11214 3.79 - 4.34: 14937 4.34 - 4.90: 24626 Nonbonded interactions: 57279 Sorted by model distance: nonbonded pdb=" O1A ADP J 401 " pdb="MG MG J 402 " model vdw 2.114 2.170 nonbonded pdb=" OH TYR I 86 " pdb=" O LEU I 158 " model vdw 2.171 3.040 nonbonded pdb=" O GLY K 229 " pdb=" OG SER K 232 " model vdw 2.215 3.040 nonbonded pdb=" OG1 THR K 221 " pdb=" O TRP K 243 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR J 178 " pdb=" OE2 GLU J 205 " model vdw 2.271 3.040 ... (remaining 57274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.002 0.031 7220 Z= 0.093 Angle : 0.526 7.635 9780 Z= 0.240 Chirality : 0.039 0.143 1085 Planarity : 0.004 0.058 1232 Dihedral : 17.063 123.547 2696 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 20.58 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.29), residues: 846 helix: 2.16 (0.26), residues: 426 sheet: 0.60 (0.73), residues: 51 loop : -0.39 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 298 TYR 0.011 0.001 TYR I 231 PHE 0.010 0.001 PHE I 90 TRP 0.010 0.001 TRP I 11 HIS 0.002 0.001 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 7220) covalent geometry : angle 0.52574 ( 9780) hydrogen bonds : bond 0.13759 ( 343) hydrogen bonds : angle 5.49625 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.265 Fit side-chains REVERT: H 281 GLN cc_start: 0.7122 (mt0) cc_final: 0.6509 (tt0) REVERT: I 97 MET cc_start: 0.5214 (ptp) cc_final: 0.4874 (mtm) REVERT: I 140 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6767 (tt) REVERT: J 42 LYS cc_start: 0.7691 (mttt) cc_final: 0.6763 (tttt) REVERT: J 43 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7095 (mm) REVERT: K 76 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6302 (mp) REVERT: K 278 LYS cc_start: 0.8506 (tmtt) cc_final: 0.7773 (ttpt) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.0645 time to fit residues: 8.9679 Evaluate side-chains 100 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 202 ASP Chi-restraints excluded: chain J residue 43 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 239 SER Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 136 GLN J 47 HIS J 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.175850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153798 restraints weight = 8245.695| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.45 r_work: 0.3718 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7220 Z= 0.152 Angle : 0.588 8.499 9780 Z= 0.278 Chirality : 0.042 0.137 1085 Planarity : 0.005 0.048 1232 Dihedral : 6.903 120.639 983 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.88 % Allowed : 19.00 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.29), residues: 846 helix: 1.91 (0.26), residues: 425 sheet: 0.38 (0.72), residues: 51 loop : -0.37 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 309 TYR 0.016 0.002 TYR I 231 PHE 0.010 0.002 PHE J 17 TRP 0.007 0.001 TRP I 11 HIS 0.004 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7220) covalent geometry : angle 0.58792 ( 9780) hydrogen bonds : bond 0.04084 ( 343) hydrogen bonds : angle 4.44107 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.178 Fit side-chains REVERT: H 281 GLN cc_start: 0.7087 (mt0) cc_final: 0.6512 (tt0) REVERT: I 140 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6709 (tt) REVERT: J 42 LYS cc_start: 0.7945 (mttt) cc_final: 0.6920 (tttt) REVERT: J 55 ILE cc_start: 0.6345 (OUTLIER) cc_final: 0.5985 (mt) REVERT: J 172 GLN cc_start: 0.4845 (mp10) cc_final: 0.4174 (mm-40) REVERT: K 76 LEU cc_start: 0.6858 (tp) cc_final: 0.6285 (mp) REVERT: K 189 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7615 (tt) REVERT: K 208 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: K 278 LYS cc_start: 0.8577 (tmtt) cc_final: 0.7807 (ttpt) outliers start: 22 outliers final: 4 residues processed: 110 average time/residue: 0.0724 time to fit residues: 11.0252 Evaluate side-chains 96 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 208 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 GLN J 47 HIS J 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152000 restraints weight = 8369.585| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.53 r_work: 0.3734 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7220 Z= 0.123 Angle : 0.554 8.142 9780 Z= 0.260 Chirality : 0.041 0.139 1085 Planarity : 0.004 0.045 1232 Dihedral : 6.256 121.865 967 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 20.18 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 846 helix: 1.84 (0.25), residues: 431 sheet: 0.16 (0.72), residues: 51 loop : -0.33 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 309 TYR 0.014 0.001 TYR I 231 PHE 0.008 0.001 PHE J 17 TRP 0.007 0.001 TRP I 11 HIS 0.004 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7220) covalent geometry : angle 0.55424 ( 9780) hydrogen bonds : bond 0.03705 ( 343) hydrogen bonds : angle 4.23333 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.180 Fit side-chains REVERT: I 263 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.5725 (pm20) REVERT: I 266 ARG cc_start: 0.7232 (tpp80) cc_final: 0.6351 (mtt180) REVERT: J 42 LYS cc_start: 0.7849 (mttt) cc_final: 0.6850 (tttt) REVERT: J 55 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5863 (mt) REVERT: J 172 GLN cc_start: 0.4817 (mp10) cc_final: 0.4261 (mm-40) REVERT: K 76 LEU cc_start: 0.6820 (tp) cc_final: 0.6236 (mp) REVERT: K 208 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: K 278 LYS cc_start: 0.8541 (tmtt) cc_final: 0.7764 (ttpt) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.0593 time to fit residues: 8.9970 Evaluate side-chains 99 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 208 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 5.9990 chunk 83 optimal weight: 0.0030 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS J 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.173000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150083 restraints weight = 8469.185| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.55 r_work: 0.3683 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7220 Z= 0.159 Angle : 0.603 7.955 9780 Z= 0.285 Chirality : 0.042 0.154 1085 Planarity : 0.005 0.045 1232 Dihedral : 6.283 122.081 965 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.67 % Allowed : 20.18 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.29), residues: 846 helix: 1.58 (0.25), residues: 425 sheet: 0.04 (0.73), residues: 51 loop : -0.43 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 188 TYR 0.015 0.002 TYR J 127 PHE 0.010 0.002 PHE J 91 TRP 0.008 0.001 TRP I 11 HIS 0.005 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7220) covalent geometry : angle 0.60315 ( 9780) hydrogen bonds : bond 0.04028 ( 343) hydrogen bonds : angle 4.36565 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.221 Fit side-chains REVERT: I 140 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6771 (tt) REVERT: I 223 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6723 (ttm-80) REVERT: I 263 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.5860 (pm20) REVERT: I 266 ARG cc_start: 0.7349 (tpp80) cc_final: 0.6526 (mtt180) REVERT: J 42 LYS cc_start: 0.7859 (mttt) cc_final: 0.6835 (tttt) REVERT: J 55 ILE cc_start: 0.6362 (OUTLIER) cc_final: 0.6010 (mt) REVERT: J 118 MET cc_start: 0.7068 (mmm) cc_final: 0.6795 (mmm) REVERT: K 63 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8090 (mt) REVERT: K 76 LEU cc_start: 0.6706 (tp) cc_final: 0.6146 (mp) REVERT: K 208 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: K 278 LYS cc_start: 0.8575 (tmtt) cc_final: 0.7749 (ttpt) outliers start: 28 outliers final: 14 residues processed: 119 average time/residue: 0.0684 time to fit residues: 11.0283 Evaluate side-chains 111 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 208 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS J 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151753 restraints weight = 8355.633| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.54 r_work: 0.3705 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7220 Z= 0.119 Angle : 0.564 8.102 9780 Z= 0.265 Chirality : 0.041 0.139 1085 Planarity : 0.004 0.044 1232 Dihedral : 6.148 121.506 965 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.80 % Allowed : 20.31 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 846 helix: 1.73 (0.25), residues: 425 sheet: -0.05 (0.73), residues: 51 loop : -0.37 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 309 TYR 0.011 0.001 TYR I 231 PHE 0.010 0.001 PHE K 117 TRP 0.006 0.001 TRP I 11 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7220) covalent geometry : angle 0.56372 ( 9780) hydrogen bonds : bond 0.03635 ( 343) hydrogen bonds : angle 4.20328 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.273 Fit side-chains REVERT: I 140 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6738 (tt) REVERT: I 223 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.6782 (ttm-80) REVERT: I 252 MET cc_start: 0.7023 (mtt) cc_final: 0.6608 (mtt) REVERT: I 263 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.5759 (pm20) REVERT: I 266 ARG cc_start: 0.7290 (tpp80) cc_final: 0.6488 (mtt180) REVERT: J 42 LYS cc_start: 0.7877 (mttt) cc_final: 0.6830 (tttt) REVERT: J 55 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5918 (mt) REVERT: J 118 MET cc_start: 0.7043 (mmm) cc_final: 0.6785 (mmm) REVERT: K 63 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8098 (mt) REVERT: K 76 LEU cc_start: 0.6829 (tp) cc_final: 0.6241 (mp) REVERT: K 189 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7630 (tt) REVERT: K 208 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: K 278 LYS cc_start: 0.8528 (tmtt) cc_final: 0.7727 (ttpt) outliers start: 29 outliers final: 15 residues processed: 118 average time/residue: 0.0604 time to fit residues: 10.0878 Evaluate side-chains 114 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 51 optimal weight: 0.8980 chunk 49 optimal weight: 0.0000 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 152 GLN J 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.173733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150762 restraints weight = 8485.880| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.56 r_work: 0.3697 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7220 Z= 0.120 Angle : 0.571 8.122 9780 Z= 0.269 Chirality : 0.041 0.138 1085 Planarity : 0.004 0.044 1232 Dihedral : 6.074 119.769 965 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.41 % Allowed : 20.58 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 846 helix: 1.70 (0.25), residues: 432 sheet: 0.00 (0.74), residues: 51 loop : -0.32 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 309 TYR 0.010 0.001 TYR I 231 PHE 0.009 0.001 PHE J 17 TRP 0.007 0.001 TRP I 11 HIS 0.003 0.001 HIS K 283 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7220) covalent geometry : angle 0.57124 ( 9780) hydrogen bonds : bond 0.03595 ( 343) hydrogen bonds : angle 4.14144 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.192 Fit side-chains REVERT: I 140 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6734 (tt) REVERT: I 223 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6836 (ttm-80) REVERT: I 252 MET cc_start: 0.7071 (mtt) cc_final: 0.6645 (mtt) REVERT: I 263 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.5853 (pm20) REVERT: I 266 ARG cc_start: 0.7284 (tpp80) cc_final: 0.6485 (mtt180) REVERT: J 42 LYS cc_start: 0.7849 (mttt) cc_final: 0.6805 (tttt) REVERT: J 55 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5871 (mt) REVERT: J 118 MET cc_start: 0.7045 (mmm) cc_final: 0.6787 (mmm) REVERT: K 63 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (mt) REVERT: K 76 LEU cc_start: 0.6838 (tp) cc_final: 0.6250 (mp) REVERT: K 189 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7598 (tt) REVERT: K 208 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7028 (mt-10) REVERT: K 278 LYS cc_start: 0.8536 (tmtt) cc_final: 0.7722 (ttpt) outliers start: 26 outliers final: 16 residues processed: 111 average time/residue: 0.0694 time to fit residues: 10.6270 Evaluate side-chains 114 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 10.0000 chunk 48 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.176749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154005 restraints weight = 8382.298| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.54 r_work: 0.3741 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7220 Z= 0.099 Angle : 0.546 8.219 9780 Z= 0.255 Chirality : 0.040 0.141 1085 Planarity : 0.004 0.045 1232 Dihedral : 5.891 117.032 965 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.36 % Allowed : 22.02 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 846 helix: 1.89 (0.25), residues: 432 sheet: 0.01 (0.74), residues: 51 loop : -0.24 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 309 TYR 0.014 0.001 TYR J 127 PHE 0.009 0.001 PHE J 17 TRP 0.005 0.001 TRP I 11 HIS 0.004 0.001 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7220) covalent geometry : angle 0.54643 ( 9780) hydrogen bonds : bond 0.03292 ( 343) hydrogen bonds : angle 4.02603 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.192 Fit side-chains REVERT: I 140 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6764 (tt) REVERT: I 252 MET cc_start: 0.7019 (mtt) cc_final: 0.6579 (mtt) REVERT: I 266 ARG cc_start: 0.7330 (tpp80) cc_final: 0.6524 (mtt180) REVERT: J 42 LYS cc_start: 0.7814 (mttt) cc_final: 0.6775 (tttt) REVERT: J 55 ILE cc_start: 0.6137 (OUTLIER) cc_final: 0.5714 (mt) REVERT: J 137 ASP cc_start: 0.8269 (t70) cc_final: 0.8049 (t0) REVERT: K 63 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8172 (mt) REVERT: K 76 LEU cc_start: 0.6863 (tp) cc_final: 0.6247 (mp) REVERT: K 189 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7439 (tt) REVERT: K 278 LYS cc_start: 0.8494 (tmtt) cc_final: 0.7694 (ttpt) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.0679 time to fit residues: 10.1463 Evaluate side-chains 106 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 94 ASN I 152 GLN I 247 GLN J 47 HIS ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.172250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149525 restraints weight = 8492.152| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.55 r_work: 0.3693 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7220 Z= 0.171 Angle : 0.631 8.018 9780 Z= 0.298 Chirality : 0.043 0.144 1085 Planarity : 0.005 0.044 1232 Dihedral : 6.209 118.210 965 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.80 % Allowed : 20.97 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 846 helix: 1.55 (0.25), residues: 425 sheet: -0.06 (0.74), residues: 51 loop : -0.46 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 309 TYR 0.018 0.002 TYR J 127 PHE 0.011 0.002 PHE J 91 TRP 0.009 0.001 TRP I 11 HIS 0.004 0.001 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7220) covalent geometry : angle 0.63143 ( 9780) hydrogen bonds : bond 0.04068 ( 343) hydrogen bonds : angle 4.31171 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.199 Fit side-chains REVERT: I 140 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6768 (tt) REVERT: I 223 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.6892 (ttm-80) REVERT: I 252 MET cc_start: 0.7048 (mtt) cc_final: 0.6603 (mtt) REVERT: I 266 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6517 (mtt180) REVERT: J 50 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6426 (mt-10) REVERT: J 55 ILE cc_start: 0.6238 (OUTLIER) cc_final: 0.5864 (mt) REVERT: J 118 MET cc_start: 0.7066 (mmm) cc_final: 0.6733 (mmm) REVERT: K 63 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8069 (mt) REVERT: K 76 LEU cc_start: 0.6921 (tp) cc_final: 0.6316 (mp) REVERT: K 208 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: K 278 LYS cc_start: 0.8563 (tmtt) cc_final: 0.7764 (ttpt) outliers start: 29 outliers final: 20 residues processed: 122 average time/residue: 0.0737 time to fit residues: 12.2133 Evaluate side-chains 121 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 189 LEU Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 94 ASN J 47 HIS ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152533 restraints weight = 8427.153| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.54 r_work: 0.3737 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7220 Z= 0.113 Angle : 0.580 8.174 9780 Z= 0.270 Chirality : 0.040 0.139 1085 Planarity : 0.004 0.044 1232 Dihedral : 6.016 117.154 965 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.15 % Allowed : 21.23 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 846 helix: 1.71 (0.25), residues: 432 sheet: 0.05 (0.75), residues: 51 loop : -0.35 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 309 TYR 0.024 0.001 TYR I 2 PHE 0.009 0.001 PHE J 17 TRP 0.006 0.001 TRP I 11 HIS 0.003 0.001 HIS K 283 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7220) covalent geometry : angle 0.57997 ( 9780) hydrogen bonds : bond 0.03459 ( 343) hydrogen bonds : angle 4.10426 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.203 Fit side-chains REVERT: I 140 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6775 (tt) REVERT: I 263 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.5837 (pm20) REVERT: I 266 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6510 (mtt180) REVERT: J 42 LYS cc_start: 0.8051 (mttm) cc_final: 0.6928 (tttt) REVERT: J 55 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5781 (mt) REVERT: J 118 MET cc_start: 0.7039 (mmm) cc_final: 0.6782 (mmm) REVERT: J 137 ASP cc_start: 0.8252 (t70) cc_final: 0.8023 (t0) REVERT: K 63 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8062 (mt) REVERT: K 76 LEU cc_start: 0.6904 (tp) cc_final: 0.6282 (mp) REVERT: K 208 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: K 278 LYS cc_start: 0.8575 (tmtt) cc_final: 0.7767 (ttpt) outliers start: 24 outliers final: 16 residues processed: 117 average time/residue: 0.0754 time to fit residues: 12.0344 Evaluate side-chains 116 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS J 56 ASN ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146841 restraints weight = 8528.892| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.58 r_work: 0.3656 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7220 Z= 0.172 Angle : 0.645 8.012 9780 Z= 0.305 Chirality : 0.043 0.147 1085 Planarity : 0.005 0.044 1232 Dihedral : 6.253 118.004 965 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.41 % Allowed : 21.23 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.29), residues: 846 helix: 1.48 (0.25), residues: 425 sheet: -0.03 (0.76), residues: 51 loop : -0.48 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 309 TYR 0.020 0.002 TYR I 2 PHE 0.010 0.002 PHE J 91 TRP 0.010 0.001 TRP I 11 HIS 0.005 0.001 HIS I 281 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7220) covalent geometry : angle 0.64513 ( 9780) hydrogen bonds : bond 0.04056 ( 343) hydrogen bonds : angle 4.32321 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.209 Fit side-chains REVERT: I 77 ARG cc_start: 0.7315 (mtm180) cc_final: 0.7023 (ttp-170) REVERT: I 140 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6722 (tt) REVERT: I 223 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6909 (ttm-80) REVERT: I 252 MET cc_start: 0.7453 (mtt) cc_final: 0.7151 (mtt) REVERT: I 263 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.5888 (pm20) REVERT: I 266 ARG cc_start: 0.7305 (tpp80) cc_final: 0.6536 (mtt180) REVERT: J 42 LYS cc_start: 0.8231 (mttm) cc_final: 0.6995 (tttt) REVERT: J 55 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.5938 (mt) REVERT: J 118 MET cc_start: 0.7058 (mmm) cc_final: 0.6734 (mmm) REVERT: K 63 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8031 (mt) REVERT: K 76 LEU cc_start: 0.6956 (tp) cc_final: 0.6343 (mp) REVERT: K 208 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: K 278 LYS cc_start: 0.8589 (tmtt) cc_final: 0.7797 (ttpt) outliers start: 26 outliers final: 19 residues processed: 116 average time/residue: 0.0755 time to fit residues: 11.8389 Evaluate side-chains 123 residues out of total 763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 258 LEU Chi-restraints excluded: chain I residue 263 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 92 ASP Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 153 LEU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 287 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 208 GLU Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 268 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 47 HIS J 56 ASN ** J 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.174204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.151642 restraints weight = 8412.559| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.52 r_work: 0.3732 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7220 Z= 0.106 Angle : 0.584 8.194 9780 Z= 0.271 Chirality : 0.040 0.139 1085 Planarity : 0.004 0.044 1232 Dihedral : 6.001 117.207 965 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.75 % Allowed : 21.89 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.29), residues: 846 helix: 1.79 (0.25), residues: 432 sheet: 0.08 (0.77), residues: 51 loop : -0.32 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 309 TYR 0.023 0.001 TYR I 2 PHE 0.009 0.001 PHE J 17 TRP 0.005 0.001 TRP J 132 HIS 0.003 0.001 HIS K 283 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7220) covalent geometry : angle 0.58387 ( 9780) hydrogen bonds : bond 0.03351 ( 343) hydrogen bonds : angle 4.04330 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1588.61 seconds wall clock time: 27 minutes 52.82 seconds (1672.82 seconds total)