Starting phenix.real_space_refine on Thu Jul 2 00:39:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjk_45634/07_2026/9cjk_45634.map" } resolution = 3.7 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= 0.002 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 P 2 5.49 5 S 8 5.16 5 C 3079 2.51 5 N 870 2.21 5 O 822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4781 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 673 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 673 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "H" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 321 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 692 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "A" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 673 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 673 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 321 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 692 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'9ED': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 1.14, per 1000 atoms: 0.24 Number of scatterers: 4781 At special positions: 0 Unit cell: (61.875, 63.525, 130.35, 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 8 16.00 P 2 15.00 O 822 8.00 N 870 7.00 C 3079 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: 0.52 Conformation dependent library (CDL) restraints added in 185.8 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1072 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 98.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'D' and resid 159 through 235 removed outlier: 3.871A pdb=" N GLU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 235 removed outlier: 4.669A pdb=" N GLN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS F 232 " --> pdb=" O PHE F 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 235 removed outlier: 3.818A pdb=" N TRP H 206 " --> pdb=" O ARG H 202 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS H 226 " --> pdb=" O MET H 222 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU H 230 " --> pdb=" O LYS H 226 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA H 231 " --> pdb=" O SER H 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 186 removed outlier: 3.669A pdb=" N GLU E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 235 removed outlier: 3.716A pdb=" N GLU E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 191 " --> pdb=" O TRP E 187 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 192 " --> pdb=" O ARG E 188 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE E 208 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 172 Processing helix chain 'A' and resid 175 through 203 removed outlier: 3.793A pdb=" N ARG A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 235 removed outlier: 3.684A pdb=" N LEU A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 235 removed outlier: 3.588A pdb=" N GLU C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS C 226 " --> pdb=" O MET C 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 209 Processing helix chain 'G' and resid 209 through 235 removed outlier: 3.667A pdb=" N ILE G 213 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G 226 " --> pdb=" O MET G 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU G 230 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA G 231 " --> pdb=" O SER G 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 235 removed outlier: 4.720A pdb=" N LEU B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 191 " --> pdb=" O TRP B 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1332 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: 0.87 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 745 1.28 - 1.41: 1284 1.41 - 1.54: 2771 1.54 - 1.67: 52 1.67 - 1.80: 17 Bond restraints: 4869 Sorted by residual: bond pdb=" C62 9ED A 301 " pdb=" C63 9ED A 301 " ideal model delta sigma weight residual 1.330 1.555 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C60 9ED A 301 " pdb=" C61 9ED A 301 " ideal model delta sigma weight residual 1.330 1.550 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C41 9ED A 301 " pdb=" C43 9ED A 301 " ideal model delta sigma weight residual 1.523 1.348 0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" CA GLN G 210 " pdb=" C GLN G 210 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.16e-02 7.43e+03 7.27e+01 bond pdb=" CA LYS B 180 " pdb=" C LYS B 180 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.32e-02 5.74e+03 5.22e+01 ... (remaining 4864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.95: 6477 6.95 - 13.89: 58 13.89 - 20.84: 7 20.84 - 27.79: 1 27.79 - 34.74: 1 Bond angle restraints: 6544 Sorted by residual: angle pdb=" C47 9ED A 301 " pdb=" C52 9ED A 301 " pdb=" C56 9ED A 301 " ideal model delta sigma weight residual 112.85 78.11 34.74 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N GLN G 210 " pdb=" CA GLN G 210 " pdb=" C GLN G 210 " ideal model delta sigma weight residual 112.68 98.08 14.60 1.33e+00 5.65e-01 1.20e+02 angle pdb=" N ASN A 183 " pdb=" CA ASN A 183 " pdb=" C ASN A 183 " ideal model delta sigma weight residual 111.04 95.10 15.94 1.55e+00 4.16e-01 1.06e+02 angle pdb=" N LEU A 209 " pdb=" CA LEU A 209 " pdb=" C LEU A 209 " ideal model delta sigma weight residual 111.36 100.30 11.06 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N VAL F 215 " pdb=" CA VAL F 215 " pdb=" C VAL F 215 " ideal model delta sigma weight residual 110.72 120.79 -10.07 1.01e+00 9.80e-01 9.94e+01 ... (remaining 6539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 2809 35.80 - 71.59: 153 71.59 - 107.39: 16 107.39 - 143.19: 2 143.19 - 178.98: 1 Dihedral angle restraints: 2981 sinusoidal: 1367 harmonic: 1614 Sorted by residual: dihedral pdb=" C ASN A 183 " pdb=" N ASN A 183 " pdb=" CA ASN A 183 " pdb=" CB ASN A 183 " ideal model delta harmonic sigma weight residual -122.60 -102.34 -20.26 0 2.50e+00 1.60e-01 6.57e+01 dihedral pdb=" C GLN B 194 " pdb=" N GLN B 194 " pdb=" CA GLN B 194 " pdb=" CB GLN B 194 " ideal model delta harmonic sigma weight residual -122.60 -139.31 16.71 0 2.50e+00 1.60e-01 4.47e+01 dihedral pdb=" N GLN B 194 " pdb=" C GLN B 194 " pdb=" CA GLN B 194 " pdb=" CB GLN B 194 " ideal model delta harmonic sigma weight residual 122.80 138.41 -15.61 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 2978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 605 0.143 - 0.285: 91 0.285 - 0.428: 15 0.428 - 0.571: 5 0.571 - 0.713: 1 Chirality restraints: 717 Sorted by residual: chirality pdb=" CA GLN B 194 " pdb=" N GLN B 194 " pdb=" C GLN B 194 " pdb=" CB GLN B 194 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA GLN C 174 " pdb=" N GLN C 174 " pdb=" C GLN C 174 " pdb=" CB GLN C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CA VAL F 215 " pdb=" N VAL F 215 " pdb=" C VAL F 215 " pdb=" CB VAL F 215 " both_signs ideal model delta sigma weight residual False 2.44 1.94 0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 714 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C51 9ED A 301 " 0.220 2.00e-02 2.50e+03 2.19e-01 4.81e+02 pdb=" C57 9ED A 301 " 0.219 2.00e-02 2.50e+03 pdb=" C62 9ED A 301 " -0.222 2.00e-02 2.50e+03 pdb=" C63 9ED A 301 " -0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 177 " 0.027 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C GLN B 177 " -0.092 2.00e-02 2.50e+03 pdb=" O GLN B 177 " 0.035 2.00e-02 2.50e+03 pdb=" N ILE B 178 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 183 " 0.025 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" CG ASN A 183 " -0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN A 183 " 0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 183 " 0.029 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 320 2.70 - 3.25: 5391 3.25 - 3.80: 7653 3.80 - 4.35: 9184 4.35 - 4.90: 15259 Nonbonded interactions: 37807 Sorted by model distance: nonbonded pdb=" NE2 GLN E 174 " pdb=" NE2 GLN B 174 " model vdw 2.146 3.200 nonbonded pdb=" OE1 GLN D 194 " pdb=" NH1 ARG B 188 " model vdw 2.163 3.120 nonbonded pdb=" OE1 GLU D 176 " pdb=" OE1 GLN E 174 " model vdw 2.197 3.040 nonbonded pdb=" O HIS D 224 " pdb=" ND1 HIS D 224 " model vdw 2.213 3.120 nonbonded pdb=" NE2 GLN D 210 " pdb=" OE1 GLN H 210 " model vdw 2.251 3.120 ... (remaining 37802 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 159 through 235) selection = (chain 'B' and resid 159 through 235) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 159 through 235) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 3.320 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.450 Find NCS groups from input model: 0.100 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 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 : 0.021 0.225 4869 Z= 1.345 Angle : 1.914 34.737 6544 Z= 1.239 Chirality : 0.112 0.713 717 Planarity : 0.015 0.219 800 Dihedral : 20.231 178.983 1909 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.33 % Favored : 98.48 % Rotamer: Outliers : 7.75 % Allowed : 10.85 % Favored : 81.40 % Cbeta Deviations : 1.31 % 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 are not related in a simple way. whole: -0.55 (0.34), residues: 528 helix: -0.25 (0.21), residues: 516 sheet: None (None), residues: 0 loop : 2.88 (1.26), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 223 TYR 0.027 0.006 TYR F 184 PHE 0.023 0.003 PHE B 192 TRP 0.037 0.003 TRP B 187 HIS 0.005 0.001 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.02092 / 1.34 ( 4869) covalent geometry : angle 1.91407 / 1.24 ( 6544) hydrogen bonds : bond 0.17020 / 11.21 ( 444) hydrogen bonds : angle 8.01135 / 5.79 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: F 187 TRP cc_start: 0.7818 (t60) cc_final: 0.7507 (t60) REVERT: F 208 ILE cc_start: 0.7443 (mt) cc_final: 0.7101 (pt) REVERT: F 209 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6836 (tt) REVERT: F 212 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7191 (mp) REVERT: E 193 ARG cc_start: 0.6360 (tmm-80) cc_final: 0.5881 (ttp-110) REVERT: A 182 GLN cc_start: 0.5952 (tt0) cc_final: 0.5450 (mm110) REVERT: A 204 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6417 (tp) REVERT: C 230 GLU cc_start: 0.4041 (OUTLIER) cc_final: 0.3616 (mt-10) REVERT: B 193 ARG cc_start: 0.6715 (ttp80) cc_final: 0.6321 (ttp-110) outliers start: 40 outliers final: 15 residues processed: 160 average time/residue: 0.1147 time to fit residues: 21.4398 Evaluate side-chains 110 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 188 ARG Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 232 LYS Chi-restraints excluded: chain G residue 200 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 179 GLN D 182 GLN ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN A 179 GLN A 183 ASN A 221 GLN C 170 GLN C 174 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.239620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.203805 restraints weight = 4732.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.204588 restraints weight = 4267.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.207676 restraints weight = 3186.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.209166 restraints weight = 2393.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.209435 restraints weight = 2133.488| |-----------------------------------------------------------------------------| r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4869 Z= 0.162 Angle : 0.647 10.638 6544 Z= 0.328 Chirality : 0.034 0.144 717 Planarity : 0.005 0.054 800 Dihedral : 13.779 111.716 721 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.62 % Allowed : 17.05 % Favored : 77.33 % 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 are not related in a simple way. whole: 3.52 (0.33), residues: 528 helix: 2.35 (0.21), residues: 514 sheet: None (None), residues: 0 loop : 1.34 (1.22), residues: 14 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 188 TYR 0.024 0.002 TYR C 184 PHE 0.014 0.002 PHE E 192 TRP 0.017 0.001 TRP E 206 HIS 0.004 0.002 HIS D 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4869) covalent geometry : angle 0.64652 / 0.33 ( 6544) hydrogen bonds : bond 0.04615 / 3.04 ( 444) hydrogen bonds : angle 3.41443 / 2.42 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.194 Fit side-chains REVERT: D 213 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6422 (mt) REVERT: F 165 GLN cc_start: 0.8029 (tp40) cc_final: 0.7610 (pt0) REVERT: F 209 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8210 (tt) REVERT: H 210 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8302 (tt0) REVERT: A 213 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6366 (mp) outliers start: 29 outliers final: 12 residues processed: 93 average time/residue: 0.0993 time to fit residues: 11.2096 Evaluate side-chains 83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 182 GLN Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4983 r_free = 0.4983 target = 0.235567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.201581 restraints weight = 4736.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.201860 restraints weight = 3909.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.205588 restraints weight = 2977.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.206225 restraints weight = 2237.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.206337 restraints weight = 2086.901| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4869 Z= 0.132 Angle : 0.515 7.596 6544 Z= 0.268 Chirality : 0.031 0.119 717 Planarity : 0.004 0.052 800 Dihedral : 10.369 107.405 682 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.68 % Allowed : 20.93 % Favored : 75.39 % 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 are not related in a simple way. whole: 4.56 (0.32), residues: 528 helix: 2.99 (0.20), residues: 516 sheet: None (None), residues: 0 loop : 1.76 (1.22), residues: 12 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 186 TYR 0.016 0.002 TYR C 184 PHE 0.017 0.001 PHE E 192 TRP 0.019 0.001 TRP F 220 HIS 0.003 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4869) covalent geometry : angle 0.51507 / 0.27 ( 6544) hydrogen bonds : bond 0.04044 / 2.69 ( 444) hydrogen bonds : angle 2.97475 / 2.12 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.200 Fit side-chains REVERT: D 213 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6431 (mt) REVERT: F 209 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8108 (tt) REVERT: E 193 ARG cc_start: 0.7328 (tmm-80) cc_final: 0.7009 (ttp-110) REVERT: A 174 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 213 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6378 (mp) REVERT: G 221 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7690 (tm-30) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 0.1004 time to fit residues: 9.9332 Evaluate side-chains 79 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN F 165 GLN ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** 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 = 0.4905 r_free = 0.4905 target = 0.227072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.193367 restraints weight = 4830.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.193621 restraints weight = 3459.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.195340 restraints weight = 3073.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.196421 restraints weight = 2493.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.196588 restraints weight = 2251.556| |-----------------------------------------------------------------------------| r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4869 Z= 0.151 Angle : 0.527 8.294 6544 Z= 0.275 Chirality : 0.033 0.121 717 Planarity : 0.004 0.039 800 Dihedral : 9.990 111.687 679 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.81 % Allowed : 21.12 % Favored : 73.06 % 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 are not related in a simple way. whole: 4.58 (0.32), residues: 528 helix: 3.03 (0.20), residues: 508 sheet: None (None), residues: 0 loop : 1.73 (0.73), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 186 TYR 0.012 0.002 TYR C 184 PHE 0.014 0.002 PHE E 192 TRP 0.013 0.001 TRP C 206 HIS 0.003 0.001 HIS B 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4869) covalent geometry : angle 0.52738 / 0.28 ( 6544) hydrogen bonds : bond 0.03965 / 2.67 ( 444) hydrogen bonds : angle 2.96366 / 2.12 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.186 Fit side-chains REVERT: D 180 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7793 (mtpt) REVERT: D 213 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6649 (mt) REVERT: F 164 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5936 (tp) REVERT: F 209 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8135 (tt) REVERT: F 210 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8634 (tm-30) REVERT: H 221 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7750 (tm-30) REVERT: E 193 ARG cc_start: 0.7232 (tmm-80) cc_final: 0.6942 (ttp-110) REVERT: A 165 GLN cc_start: 0.8144 (tp40) cc_final: 0.7505 (tt0) REVERT: A 174 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8503 (tm-30) REVERT: A 213 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6508 (mp) outliers start: 30 outliers final: 17 residues processed: 87 average time/residue: 0.1052 time to fit residues: 10.9604 Evaluate side-chains 84 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 184 TYR Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.0370 chunk 30 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN C 185 GLN ** B 177 GLN ** 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 = 0.4910 r_free = 0.4910 target = 0.225803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.193737 restraints weight = 4838.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.194571 restraints weight = 3276.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.195365 restraints weight = 2612.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.195902 restraints weight = 2494.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.196375 restraints weight = 2265.952| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4869 Z= 0.123 Angle : 0.463 6.628 6544 Z= 0.249 Chirality : 0.031 0.125 717 Planarity : 0.003 0.036 800 Dihedral : 9.610 110.841 679 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.43 % Allowed : 22.29 % Favored : 72.29 % 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 are not related in a simple way. whole: 5.07 (0.31), residues: 528 helix: 3.35 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 1.94 (0.68), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 186 TYR 0.009 0.002 TYR F 184 PHE 0.013 0.001 PHE E 192 TRP 0.019 0.001 TRP F 220 HIS 0.004 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4869) covalent geometry : angle 0.46299 / 0.25 ( 6544) hydrogen bonds : bond 0.03666 / 2.46 ( 444) hydrogen bonds : angle 2.81344 / 2.01 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.176 Fit side-chains REVERT: D 180 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7838 (mtpt) REVERT: D 213 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6665 (mp) REVERT: F 209 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8092 (tt) REVERT: H 221 GLN cc_start: 0.8063 (tm-30) cc_final: 0.7786 (tm-30) REVERT: E 170 GLN cc_start: 0.7188 (mt0) cc_final: 0.6753 (mt0) REVERT: E 193 ARG cc_start: 0.7152 (tmm-80) cc_final: 0.6885 (ttp-110) REVERT: A 165 GLN cc_start: 0.7982 (tp40) cc_final: 0.7516 (tt0) REVERT: A 213 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6422 (mp) outliers start: 28 outliers final: 14 residues processed: 83 average time/residue: 0.0848 time to fit residues: 8.6424 Evaluate side-chains 79 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.220138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.182564 restraints weight = 5026.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.186674 restraints weight = 3295.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.189390 restraints weight = 2535.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.190787 restraints weight = 2166.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.191128 restraints weight = 1977.021| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4869 Z= 0.172 Angle : 0.543 6.446 6544 Z= 0.290 Chirality : 0.034 0.137 717 Planarity : 0.003 0.039 800 Dihedral : 10.367 114.453 679 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.20 % Allowed : 22.29 % Favored : 71.51 % 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 are not related in a simple way. whole: 4.67 (0.31), residues: 528 helix: 3.09 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 1.88 (0.70), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 186 TYR 0.009 0.002 TYR C 184 PHE 0.010 0.002 PHE E 192 TRP 0.021 0.002 TRP D 187 HIS 0.007 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 4869) covalent geometry : angle 0.54302 / 0.29 ( 6544) hydrogen bonds : bond 0.03970 / 2.66 ( 444) hydrogen bonds : angle 2.99687 / 2.15 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.169 Fit side-chains REVERT: D 180 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7870 (mtpt) REVERT: D 213 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6632 (mt) REVERT: F 186 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7905 (ttm-80) REVERT: F 209 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8136 (tt) REVERT: E 170 GLN cc_start: 0.7275 (mt0) cc_final: 0.7012 (mt0) REVERT: E 193 ARG cc_start: 0.7175 (tmm-80) cc_final: 0.6890 (ttp-110) REVERT: E 221 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6427 (tt0) REVERT: A 213 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6390 (mp) REVERT: B 221 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6533 (tt0) outliers start: 32 outliers final: 23 residues processed: 87 average time/residue: 0.0905 time to fit residues: 9.5666 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 204 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 221 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.221758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.187908 restraints weight = 4849.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.188216 restraints weight = 3559.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.190284 restraints weight = 3078.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.190905 restraints weight = 2468.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.191109 restraints weight = 2279.077| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4869 Z= 0.140 Angle : 0.503 7.485 6544 Z= 0.271 Chirality : 0.032 0.151 717 Planarity : 0.003 0.038 800 Dihedral : 10.259 113.714 679 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 5.23 % Allowed : 24.42 % Favored : 70.35 % 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 are not related in a simple way. whole: 4.97 (0.31), residues: 528 helix: 3.26 (0.20), residues: 504 sheet: None (None), residues: 0 loop : 2.64 (0.78), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 186 TYR 0.007 0.002 TYR F 184 PHE 0.011 0.001 PHE E 192 TRP 0.017 0.001 TRP D 187 HIS 0.006 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 4869) covalent geometry : angle 0.50283 / 0.27 ( 6544) hydrogen bonds : bond 0.03795 / 2.56 ( 444) hydrogen bonds : angle 2.91941 / 2.10 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.189 Fit side-chains REVERT: D 180 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7827 (mtpt) REVERT: D 213 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6625 (mt) REVERT: F 209 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8202 (tt) REVERT: F 222 MET cc_start: 0.7835 (tpt) cc_final: 0.7574 (tpt) REVERT: E 193 ARG cc_start: 0.7078 (tmm-80) cc_final: 0.6758 (ttm170) REVERT: E 221 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: A 163 GLU cc_start: 0.7961 (pm20) cc_final: 0.7565 (pm20) REVERT: A 213 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6375 (mp) REVERT: B 178 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7223 (tt) outliers start: 27 outliers final: 18 residues processed: 85 average time/residue: 0.0925 time to fit residues: 9.3849 Evaluate side-chains 86 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.221358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.187669 restraints weight = 4955.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.188804 restraints weight = 3435.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.190340 restraints weight = 2956.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.191034 restraints weight = 2418.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.191244 restraints weight = 2207.483| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4869 Z= 0.138 Angle : 0.505 8.617 6544 Z= 0.272 Chirality : 0.033 0.174 717 Planarity : 0.003 0.040 800 Dihedral : 9.990 112.266 679 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 5.62 % Allowed : 24.22 % Favored : 70.16 % 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 are not related in a simple way. whole: 4.90 (0.31), residues: 528 helix: 3.23 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 1.98 (0.73), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 186 TYR 0.011 0.002 TYR C 184 PHE 0.011 0.001 PHE E 192 TRP 0.028 0.001 TRP D 187 HIS 0.007 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 4869) covalent geometry : angle 0.50511 / 0.27 ( 6544) hydrogen bonds : bond 0.03734 / 2.50 ( 444) hydrogen bonds : angle 2.93651 / 2.11 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.180 Fit side-chains REVERT: D 163 GLU cc_start: 0.7836 (pm20) cc_final: 0.7563 (pm20) REVERT: D 180 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7781 (mtpt) REVERT: D 213 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6541 (mp) REVERT: F 209 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8163 (tt) REVERT: H 221 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7771 (mt0) REVERT: E 170 GLN cc_start: 0.7287 (mt0) cc_final: 0.6822 (mt0) REVERT: E 193 ARG cc_start: 0.7036 (tmm-80) cc_final: 0.6694 (ttm170) REVERT: E 221 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6403 (tt0) REVERT: A 163 GLU cc_start: 0.7972 (pm20) cc_final: 0.7589 (pm20) REVERT: A 213 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6373 (mp) REVERT: G 221 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7819 (mt0) REVERT: B 178 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7087 (tt) outliers start: 29 outliers final: 21 residues processed: 86 average time/residue: 0.0832 time to fit residues: 8.7333 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN H 221 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** G 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** 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 = 0.4839 r_free = 0.4839 target = 0.219562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.186383 restraints weight = 4930.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.187404 restraints weight = 3756.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.188440 restraints weight = 2841.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.189121 restraints weight = 2706.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.189641 restraints weight = 2372.196| |-----------------------------------------------------------------------------| r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4869 Z= 0.159 Angle : 0.538 7.573 6544 Z= 0.287 Chirality : 0.034 0.163 717 Planarity : 0.004 0.038 800 Dihedral : 10.107 113.017 679 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 5.43 % Allowed : 24.61 % Favored : 69.96 % 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 are not related in a simple way. whole: 4.60 (0.31), residues: 528 helix: 3.04 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 2.00 (0.75), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 186 TYR 0.006 0.002 TYR C 184 PHE 0.011 0.001 PHE E 192 TRP 0.054 0.002 TRP D 187 HIS 0.006 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 4869) covalent geometry : angle 0.53754 / 0.29 ( 6544) hydrogen bonds : bond 0.03823 / 2.57 ( 444) hydrogen bonds : angle 3.05329 / 2.20 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: D 180 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7783 (mtpt) REVERT: D 213 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6615 (mp) REVERT: F 209 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8263 (tt) REVERT: E 193 ARG cc_start: 0.7053 (tmm-80) cc_final: 0.6763 (ttm170) REVERT: A 163 GLU cc_start: 0.7894 (pm20) cc_final: 0.7503 (pm20) REVERT: A 213 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6430 (mp) REVERT: B 178 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7180 (tt) outliers start: 28 outliers final: 24 residues processed: 85 average time/residue: 0.1052 time to fit residues: 10.8570 Evaluate side-chains 89 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 178 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.222878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.189047 restraints weight = 4838.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.189672 restraints weight = 3558.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.192020 restraints weight = 2942.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.192722 restraints weight = 2331.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.192791 restraints weight = 2148.626| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4869 Z= 0.139 Angle : 0.521 8.650 6544 Z= 0.280 Chirality : 0.033 0.155 717 Planarity : 0.003 0.037 800 Dihedral : 9.727 111.816 679 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.07 % Allowed : 25.78 % Favored : 70.16 % 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 are not related in a simple way. whole: 4.72 (0.31), residues: 528 helix: 3.12 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 1.92 (0.70), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 186 TYR 0.018 0.002 TYR C 184 PHE 0.012 0.001 PHE E 192 TRP 0.045 0.002 TRP D 187 HIS 0.007 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 4869) covalent geometry : angle 0.52074 / 0.28 ( 6544) hydrogen bonds : bond 0.03857 / 2.58 ( 444) hydrogen bonds : angle 3.03721 / 2.18 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.183 Fit side-chains REVERT: D 180 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7815 (mtpt) REVERT: D 213 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6683 (mp) REVERT: E 193 ARG cc_start: 0.7003 (tmm-80) cc_final: 0.6762 (ttm170) REVERT: A 163 GLU cc_start: 0.7710 (pm20) cc_final: 0.7345 (pm20) REVERT: A 213 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6415 (mp) REVERT: B 178 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7211 (tt) outliers start: 21 outliers final: 16 residues processed: 79 average time/residue: 0.1085 time to fit residues: 10.1959 Evaluate side-chains 79 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 210 GLN Chi-restraints excluded: chain F residue 214 LEU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 178 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN C 221 GLN ** B 177 GLN ** 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 = 0.4863 r_free = 0.4863 target = 0.222348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.184477 restraints weight = 4921.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.188516 restraints weight = 3243.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.191298 restraints weight = 2515.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.192689 restraints weight = 2140.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.193797 restraints weight = 1954.495| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4869 Z= 0.149 Angle : 0.554 8.750 6544 Z= 0.295 Chirality : 0.034 0.172 717 Planarity : 0.003 0.040 800 Dihedral : 9.545 111.293 677 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.65 % Allowed : 25.00 % Favored : 70.35 % 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 are not related in a simple way. whole: 4.61 (0.31), residues: 528 helix: 3.06 (0.20), residues: 506 sheet: None (None), residues: 0 loop : 1.52 (0.64), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 186 TYR 0.028 0.003 TYR C 184 PHE 0.011 0.001 PHE E 192 TRP 0.046 0.002 TRP D 187 HIS 0.005 0.001 HIS G 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 4869) covalent geometry : angle 0.55431 / 0.29 ( 6544) hydrogen bonds : bond 0.03931 / 2.61 ( 444) hydrogen bonds : angle 3.09294 / 2.21 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 866.96 seconds wall clock time: 15 minutes 41.76 seconds (941.76 seconds total)