Starting phenix.real_space_refine on Wed Sep 17 05:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.map" model { file = "/net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e7u_47690/09_2025/9e7u_47690.cif" } 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= 0.015 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 26 5.16 5 C 3113 2.51 5 N 802 2.21 5 O 925 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4867 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2102 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 5, 'TRANS': 252} Chain: "A" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1835 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 9, 'TRANS': 215} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.43, per 1000 atoms: 0.29 Number of scatterers: 4867 At special positions: 0 Unit cell: (67.344, 84.18, 109.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 Mg 1 11.99 O 925 8.00 N 802 7.00 C 3113 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: 0.40 Conformation dependent library (CDL) restraints added in 189.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 54.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.721A pdb=" N GLU C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.554A pdb=" N ARG C 28 " --> pdb=" O MET C 24 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 70 removed outlier: 3.626A pdb=" N ASN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 120 removed outlier: 4.164A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.698A pdb=" N GLU C 128 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.889A pdb=" N THR C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.960A pdb=" N MET C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.826A pdb=" N ILE C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.534A pdb=" N ASP C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.956A pdb=" N LEU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 243 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 83 through 95 removed outlier: 3.916A pdb=" N ILE A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.583A pdb=" N LYS B1098 " --> pdb=" O ASN B1094 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B1100 " --> pdb=" O GLN B1096 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B1105 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1122 Processing helix chain 'B' and resid 1126 through 1138 removed outlier: 3.506A pdb=" N ARG B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1146 through 1157 Processing helix chain 'B' and resid 1158 through 1178 Processing helix chain 'B' and resid 1185 through 1203 Processing helix chain 'B' and resid 1216 through 1228 Processing helix chain 'B' and resid 1229 through 1245 removed outlier: 3.737A pdb=" N LEU B1233 " --> pdb=" O GLN B1229 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B1234 " --> pdb=" O GLN B1230 " (cutoff:3.500A) Proline residue: B1237 - end of helix removed outlier: 4.270A pdb=" N SER B1245 " --> pdb=" O LYS B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1249 Processing helix chain 'B' and resid 1256 through 1272 removed outlier: 3.568A pdb=" N VAL B1265 " --> pdb=" O ALA B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1276 through 1290 Processing helix chain 'B' and resid 1301 through 1304 Processing helix chain 'B' and resid 1305 through 1311 removed outlier: 3.698A pdb=" N ASN B1311 " --> pdb=" O ASP B1307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 15 removed outlier: 6.482A pdb=" N CYS C 13 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN C 98 " --> pdb=" O CYS C 13 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C 15 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 37 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 50 removed outlier: 6.340A pdb=" N LEU A 12 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 33 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 14 " --> pdb=" O ILE A 31 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 642 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: 0.63 Time building geometry restraints manager: 0.55 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: 1577 1.34 - 1.46: 1016 1.46 - 1.58: 2319 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 4956 Sorted by residual: bond pdb=" CB ASP A 84 " pdb=" CG ASP A 84 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.35e+00 bond pdb=" CB ASP C 248 " pdb=" CG ASP C 248 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.99e+00 bond pdb=" CB VAL C 47 " pdb=" CG2 VAL C 47 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" C PRO B1254 " pdb=" N PRO B1255 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.83e+00 bond pdb=" CB LYS B1123 " pdb=" CG LYS B1123 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 ... (remaining 4951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 6508 1.68 - 3.35: 144 3.35 - 5.03: 23 5.03 - 6.70: 7 6.70 - 8.38: 4 Bond angle restraints: 6686 Sorted by residual: angle pdb=" CA LYS B1123 " pdb=" CB LYS B1123 " pdb=" CG LYS B1123 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N VAL A 49 " pdb=" CA VAL A 49 " pdb=" C VAL A 49 " ideal model delta sigma weight residual 112.04 107.04 5.00 1.40e+00 5.10e-01 1.27e+01 angle pdb=" N ILE A 122 " pdb=" CA ILE A 122 " pdb=" C ILE A 122 " ideal model delta sigma weight residual 113.39 108.66 4.73 1.47e+00 4.63e-01 1.03e+01 angle pdb=" N SER C 201 " pdb=" CA SER C 201 " pdb=" C SER C 201 " ideal model delta sigma weight residual 114.09 109.58 4.51 1.55e+00 4.16e-01 8.48e+00 angle pdb=" CB LYS B1123 " pdb=" CG LYS B1123 " pdb=" CD LYS B1123 " ideal model delta sigma weight residual 111.30 117.81 -6.51 2.30e+00 1.89e-01 8.00e+00 ... (remaining 6681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2486 17.86 - 35.73: 377 35.73 - 53.59: 114 53.59 - 71.45: 21 71.45 - 89.32: 8 Dihedral angle restraints: 3006 sinusoidal: 1242 harmonic: 1764 Sorted by residual: dihedral pdb=" CA PRO C 89 " pdb=" C PRO C 89 " pdb=" N SER C 90 " pdb=" CA SER C 90 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LYS C 200 " pdb=" C LYS C 200 " pdb=" N SER C 201 " pdb=" CA SER C 201 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL B1139 " pdb=" C VAL B1139 " pdb=" N SER B1140 " pdb=" CA SER B1140 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 456 0.032 - 0.063: 218 0.063 - 0.095: 48 0.095 - 0.127: 26 0.127 - 0.159: 3 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ILE C 12 " pdb=" N ILE C 12 " pdb=" C ILE C 12 " pdb=" CB ILE C 12 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA PRO C 44 " pdb=" N PRO C 44 " pdb=" C PRO C 44 " pdb=" CB PRO C 44 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA PRO C 89 " pdb=" N PRO C 89 " pdb=" C PRO C 89 " pdb=" CB PRO C 89 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 748 not shown) Planarity restraints: 854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 248 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ASP C 248 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP C 248 " -0.015 2.00e-02 2.50e+03 pdb=" N SER C 249 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 111 " -0.011 2.00e-02 2.50e+03 1.39e-02 3.40e+00 pdb=" CG PHE A 111 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 111 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 111 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 111 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B1253 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B1254 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B1254 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1254 " -0.024 5.00e-02 4.00e+02 ... (remaining 851 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 33 2.55 - 3.14: 3655 3.14 - 3.73: 7357 3.73 - 4.31: 9890 4.31 - 4.90: 17246 Nonbonded interactions: 38181 Sorted by model distance: nonbonded pdb=" OE2 GLU C 42 " pdb="MG MG C 301 " model vdw 1.963 2.170 nonbonded pdb=" OD1 ASN B1207 " pdb=" OG SER B1249 " model vdw 2.222 3.040 nonbonded pdb=" O SER C 56 " pdb=" N ASP C 59 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A 83 " pdb=" ND1 HIS A 86 " model vdw 2.241 3.120 nonbonded pdb=" OH TYR C 62 " pdb=" O PRO C 175 " model vdw 2.243 3.040 ... (remaining 38176 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.005 0.045 4956 Z= 0.203 Angle : 0.653 8.375 6686 Z= 0.354 Chirality : 0.041 0.159 751 Planarity : 0.004 0.044 854 Dihedral : 18.980 89.318 1860 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.93 % Allowed : 26.28 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.77 (0.35), residues: 593 helix: 0.61 (0.31), residues: 302 sheet: 0.13 (0.69), residues: 59 loop : -2.24 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.012 0.001 TYR B1234 PHE 0.032 0.002 PHE A 111 TRP 0.008 0.002 TRP C 95 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 4956) covalent geometry : angle 0.65323 ( 6686) hydrogen bonds : bond 0.13614 ( 221) hydrogen bonds : angle 6.16588 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 LEU cc_start: 0.8446 (mt) cc_final: 0.8239 (mt) REVERT: C 152 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7891 (mmtp) REVERT: C 200 LYS cc_start: 0.8529 (ptmm) cc_final: 0.8188 (ptmm) REVERT: C 230 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: A 39 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5388 (p0) REVERT: A 55 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7975 (pp) REVERT: B 1193 LYS cc_start: 0.7669 (mtmm) cc_final: 0.7374 (mtpt) outliers start: 27 outliers final: 22 residues processed: 151 average time/residue: 0.0796 time to fit residues: 15.2414 Evaluate side-chains 160 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 1107 SER Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1121 THR Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1306 LYS Chi-restraints excluded: chain B residue 1313 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN C 96 GLN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118283 restraints weight = 6874.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121347 restraints weight = 3497.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123315 restraints weight = 2107.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124512 restraints weight = 1431.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125456 restraints weight = 1067.092| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4956 Z= 0.137 Angle : 0.546 7.439 6686 Z= 0.285 Chirality : 0.039 0.145 751 Planarity : 0.005 0.047 854 Dihedral : 9.132 59.856 690 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.56 % Allowed : 25.91 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.68 (0.35), residues: 593 helix: 0.73 (0.31), residues: 310 sheet: 0.22 (0.69), residues: 59 loop : -2.40 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 223 TYR 0.009 0.001 TYR C 62 PHE 0.020 0.002 PHE A 111 TRP 0.007 0.001 TRP C 95 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4956) covalent geometry : angle 0.54637 ( 6686) hydrogen bonds : bond 0.03727 ( 221) hydrogen bonds : angle 4.51582 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 LEU cc_start: 0.8443 (mt) cc_final: 0.8239 (mt) REVERT: C 84 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: C 230 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: A 55 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7915 (pp) REVERT: B 1193 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7321 (mtpt) outliers start: 25 outliers final: 13 residues processed: 142 average time/residue: 0.0879 time to fit residues: 15.6093 Evaluate side-chains 139 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN B1256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120360 restraints weight = 6849.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123252 restraints weight = 3668.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125150 restraints weight = 2285.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126387 restraints weight = 1573.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127220 restraints weight = 1174.789| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4956 Z= 0.126 Angle : 0.534 9.784 6686 Z= 0.275 Chirality : 0.040 0.253 751 Planarity : 0.004 0.049 854 Dihedral : 7.584 58.099 658 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.11 % Allowed : 24.82 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.52 (0.35), residues: 593 helix: 0.88 (0.31), residues: 309 sheet: 0.45 (0.70), residues: 59 loop : -2.39 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 240 TYR 0.010 0.001 TYR C 36 PHE 0.030 0.002 PHE C 238 TRP 0.013 0.002 TRP C 95 HIS 0.002 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4956) covalent geometry : angle 0.53383 ( 6686) hydrogen bonds : bond 0.03403 ( 221) hydrogen bonds : angle 4.35409 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: C 230 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: A 55 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7844 (pp) REVERT: B 1193 LYS cc_start: 0.7654 (mtmm) cc_final: 0.7357 (mtpt) outliers start: 28 outliers final: 18 residues processed: 139 average time/residue: 0.0825 time to fit residues: 14.3409 Evaluate side-chains 140 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1314 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** B1256 ASN ** 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 = 0.3621 r_free = 0.3621 target = 0.127850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117029 restraints weight = 6820.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119928 restraints weight = 3573.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121762 restraints weight = 2186.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122938 restraints weight = 1504.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123771 restraints weight = 1121.162| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4956 Z= 0.210 Angle : 0.575 8.227 6686 Z= 0.297 Chirality : 0.042 0.205 751 Planarity : 0.005 0.051 854 Dihedral : 7.649 58.794 657 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.93 % Allowed : 25.91 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.56 (0.34), residues: 593 helix: 0.85 (0.31), residues: 304 sheet: 0.42 (0.68), residues: 59 loop : -2.33 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.014 0.002 TYR B1234 PHE 0.023 0.002 PHE C 238 TRP 0.009 0.002 TRP C 95 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 4956) covalent geometry : angle 0.57498 ( 6686) hydrogen bonds : bond 0.03919 ( 221) hydrogen bonds : angle 4.40665 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: C 84 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: C 122 GLN cc_start: 0.6822 (mt0) cc_final: 0.6567 (mt0) REVERT: C 200 LYS cc_start: 0.8579 (ptmm) cc_final: 0.8233 (ptmm) REVERT: A 55 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7890 (pp) REVERT: B 1193 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7357 (mtpt) outliers start: 27 outliers final: 18 residues processed: 156 average time/residue: 0.0779 time to fit residues: 15.4813 Evaluate side-chains 158 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN C 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.127341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116181 restraints weight = 6958.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119218 restraints weight = 3568.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121084 restraints weight = 2161.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122364 restraints weight = 1477.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123127 restraints weight = 1094.148| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4956 Z= 0.220 Angle : 0.590 7.899 6686 Z= 0.302 Chirality : 0.043 0.230 751 Planarity : 0.005 0.051 854 Dihedral : 7.292 58.295 655 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.11 % Allowed : 27.01 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.62 (0.34), residues: 593 helix: 0.79 (0.31), residues: 304 sheet: 0.22 (0.66), residues: 59 loop : -2.29 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.015 0.002 TYR C 36 PHE 0.026 0.002 PHE C 238 TRP 0.009 0.002 TRP C 95 HIS 0.005 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 4956) covalent geometry : angle 0.58951 ( 6686) hydrogen bonds : bond 0.03940 ( 221) hydrogen bonds : angle 4.41497 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8617 (mt) cc_final: 0.8363 (mp) REVERT: C 84 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: C 122 GLN cc_start: 0.6864 (mt0) cc_final: 0.6581 (mt0) REVERT: C 124 GLN cc_start: 0.8196 (tp40) cc_final: 0.7981 (tp40) REVERT: C 200 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8219 (ptmm) REVERT: A 55 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7882 (pp) REVERT: B 1193 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7353 (mtpt) REVERT: B 1309 LEU cc_start: 0.8570 (mt) cc_final: 0.8315 (mp) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.0848 time to fit residues: 16.8789 Evaluate side-chains 164 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN C 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119234 restraints weight = 6985.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122111 restraints weight = 3624.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123824 restraints weight = 2210.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125129 restraints weight = 1534.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125890 restraints weight = 1128.321| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4956 Z= 0.172 Angle : 0.564 7.464 6686 Z= 0.289 Chirality : 0.042 0.246 751 Planarity : 0.005 0.050 854 Dihedral : 7.050 58.494 653 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.29 % Allowed : 27.74 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.55 (0.34), residues: 593 helix: 0.90 (0.31), residues: 304 sheet: 0.09 (0.67), residues: 59 loop : -2.30 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.013 0.001 TYR C 36 PHE 0.027 0.002 PHE C 238 TRP 0.008 0.001 TRP C 95 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4956) covalent geometry : angle 0.56441 ( 6686) hydrogen bonds : bond 0.03653 ( 221) hydrogen bonds : angle 4.30772 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8602 (mt) cc_final: 0.8335 (mp) REVERT: C 84 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: C 122 GLN cc_start: 0.6871 (mt0) cc_final: 0.6608 (mt0) REVERT: C 124 GLN cc_start: 0.8176 (tp40) cc_final: 0.7964 (tp40) REVERT: A 55 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7859 (pp) REVERT: B 1193 LYS cc_start: 0.7673 (mtmm) cc_final: 0.7345 (mtpt) REVERT: B 1309 LEU cc_start: 0.8579 (mt) cc_final: 0.8322 (mp) outliers start: 29 outliers final: 20 residues processed: 155 average time/residue: 0.0783 time to fit residues: 15.3436 Evaluate side-chains 160 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 GLN C 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115439 restraints weight = 6800.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118188 restraints weight = 3644.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119951 restraints weight = 2285.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120973 restraints weight = 1587.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121906 restraints weight = 1221.563| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 4956 Z= 0.279 Angle : 0.643 8.221 6686 Z= 0.327 Chirality : 0.046 0.229 751 Planarity : 0.005 0.049 854 Dihedral : 7.308 59.960 653 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.47 % Allowed : 29.01 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.85 (0.34), residues: 593 helix: 0.62 (0.31), residues: 304 sheet: -0.13 (0.66), residues: 59 loop : -2.35 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 240 TYR 0.017 0.002 TYR C 36 PHE 0.034 0.002 PHE C 238 TRP 0.011 0.002 TRP C 95 HIS 0.005 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00674 ( 4956) covalent geometry : angle 0.64320 ( 6686) hydrogen bonds : bond 0.04356 ( 221) hydrogen bonds : angle 4.48622 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 32 LEU cc_start: 0.8624 (mt) cc_final: 0.8356 (mp) REVERT: C 84 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: C 124 GLN cc_start: 0.8200 (tp40) cc_final: 0.7939 (tp40) REVERT: A 4 LEU cc_start: 0.7955 (tp) cc_final: 0.7708 (tt) REVERT: A 55 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7879 (pp) REVERT: B 1193 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7311 (mtpp) REVERT: B 1309 LEU cc_start: 0.8642 (mt) cc_final: 0.8389 (mp) outliers start: 30 outliers final: 22 residues processed: 158 average time/residue: 0.0793 time to fit residues: 15.8885 Evaluate side-chains 167 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 43 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN C 210 GLN C 215 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119479 restraints weight = 6906.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122413 restraints weight = 3654.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124345 restraints weight = 2275.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125562 restraints weight = 1579.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126483 restraints weight = 1188.358| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4956 Z= 0.181 Angle : 0.598 9.659 6686 Z= 0.303 Chirality : 0.043 0.275 751 Planarity : 0.005 0.048 854 Dihedral : 7.141 59.999 653 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.74 % Allowed : 30.47 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.73 (0.34), residues: 593 helix: 0.75 (0.31), residues: 304 sheet: -0.13 (0.66), residues: 59 loop : -2.33 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.012 0.001 TYR C 36 PHE 0.029 0.002 PHE C 238 TRP 0.008 0.002 TRP C 95 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 4956) covalent geometry : angle 0.59769 ( 6686) hydrogen bonds : bond 0.03714 ( 221) hydrogen bonds : angle 4.32027 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.6769 (mt-10) cc_final: 0.6466 (mp0) REVERT: C 124 GLN cc_start: 0.8156 (tp40) cc_final: 0.7891 (tp40) REVERT: C 240 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7515 (mtp180) REVERT: A 55 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7829 (pp) REVERT: B 1193 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7336 (mtpt) REVERT: B 1309 LEU cc_start: 0.8635 (mt) cc_final: 0.8382 (mp) outliers start: 26 outliers final: 24 residues processed: 154 average time/residue: 0.0780 time to fit residues: 15.1966 Evaluate side-chains 161 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1306 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 55 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN C 210 GLN C 215 GLN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.129633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118799 restraints weight = 6866.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121720 restraints weight = 3562.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123560 restraints weight = 2169.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124691 restraints weight = 1488.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125581 restraints weight = 1120.122| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4956 Z= 0.174 Angle : 0.605 9.397 6686 Z= 0.305 Chirality : 0.043 0.258 751 Planarity : 0.005 0.046 854 Dihedral : 7.035 59.871 653 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.29 % Allowed : 29.93 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.34), residues: 593 helix: 0.80 (0.31), residues: 304 sheet: -0.18 (0.66), residues: 59 loop : -2.31 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.013 0.001 TYR C 36 PHE 0.038 0.002 PHE C 238 TRP 0.008 0.001 TRP C 95 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 4956) covalent geometry : angle 0.60521 ( 6686) hydrogen bonds : bond 0.03672 ( 221) hydrogen bonds : angle 4.28025 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6472 (mp0) REVERT: C 124 GLN cc_start: 0.8149 (tp40) cc_final: 0.7887 (tp40) REVERT: A 4 LEU cc_start: 0.7957 (tp) cc_final: 0.7675 (tt) REVERT: A 55 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7818 (pp) REVERT: B 1193 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7355 (mtpt) REVERT: B 1309 LEU cc_start: 0.8650 (mt) cc_final: 0.8410 (mp) outliers start: 29 outliers final: 25 residues processed: 152 average time/residue: 0.0820 time to fit residues: 15.6839 Evaluate side-chains 161 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1306 LYS Chi-restraints excluded: chain B residue 1314 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN C 210 GLN C 215 GLN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117753 restraints weight = 6834.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120601 restraints weight = 3571.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122500 restraints weight = 2211.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123737 restraints weight = 1518.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124592 restraints weight = 1122.688| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4956 Z= 0.160 Angle : 0.595 9.237 6686 Z= 0.300 Chirality : 0.043 0.259 751 Planarity : 0.005 0.046 854 Dihedral : 6.838 59.961 651 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.74 % Allowed : 30.66 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.61 (0.35), residues: 593 helix: 0.87 (0.31), residues: 304 sheet: -0.16 (0.68), residues: 59 loop : -2.29 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.011 0.001 TYR C 36 PHE 0.035 0.002 PHE C 238 TRP 0.009 0.001 TRP C 95 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4956) covalent geometry : angle 0.59481 ( 6686) hydrogen bonds : bond 0.03525 ( 221) hydrogen bonds : angle 4.24302 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.7559 (tmm) cc_final: 0.7260 (ttp) REVERT: C 84 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6529 (mp0) REVERT: C 124 GLN cc_start: 0.8153 (tp40) cc_final: 0.7881 (tp40) REVERT: C 240 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7520 (mtp180) REVERT: A 4 LEU cc_start: 0.7973 (tp) cc_final: 0.7665 (tt) REVERT: A 55 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7842 (pp) REVERT: B 1193 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7325 (mtpt) REVERT: B 1309 LEU cc_start: 0.8633 (mt) cc_final: 0.8385 (mp) outliers start: 26 outliers final: 24 residues processed: 148 average time/residue: 0.0822 time to fit residues: 15.2544 Evaluate side-chains 157 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 1116 GLU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1139 VAL Chi-restraints excluded: chain B residue 1172 ASN Chi-restraints excluded: chain B residue 1173 ILE Chi-restraints excluded: chain B residue 1176 LEU Chi-restraints excluded: chain B residue 1180 ASP Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1275 LEU Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1290 LEU Chi-restraints excluded: chain B residue 1302 LEU Chi-restraints excluded: chain B residue 1306 LYS Chi-restraints excluded: chain B residue 1314 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN C 215 GLN ** B1256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120279 restraints weight = 6847.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123172 restraints weight = 3612.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125097 restraints weight = 2239.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126342 restraints weight = 1548.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.127110 restraints weight = 1153.045| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4956 Z= 0.155 Angle : 0.590 9.083 6686 Z= 0.296 Chirality : 0.042 0.241 751 Planarity : 0.005 0.047 854 Dihedral : 6.729 59.989 651 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.56 % Allowed : 31.02 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.54 (0.35), residues: 593 helix: 0.95 (0.32), residues: 304 sheet: -0.14 (0.68), residues: 59 loop : -2.27 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 240 TYR 0.011 0.001 TYR C 36 PHE 0.034 0.002 PHE C 238 TRP 0.009 0.001 TRP C 95 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4956) covalent geometry : angle 0.58961 ( 6686) hydrogen bonds : bond 0.03463 ( 221) hydrogen bonds : angle 4.20770 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.66 seconds wall clock time: 19 minutes 20.32 seconds (1160.32 seconds total)