Starting phenix.real_space_refine on Tue Mar 3 19:10:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cr1_30444/03_2026/7cr1_30444.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 36 5.16 5 Cl 4 4.86 5 C 5464 2.51 5 N 1384 2.21 5 O 1328 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8220 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'GB9': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8220 At special positions: 0 Unit cell: (124.722, 124.722, 75.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 36 16.00 F 4 9.00 O 1328 8.00 N 1384 7.00 C 5464 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: 0.88 Conformation dependent library (CDL) restraints added in 296.6 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 85.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 115 removed outlier: 4.155A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.979A pdb=" N CYS A 151 " --> pdb=" O ALA A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.805A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 329 removed outlier: 3.827A pdb=" N GLY A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 147 Processing helix chain 'B' and resid 148 through 151 removed outlier: 3.979A pdb=" N CYS B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 157 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR C 95 " --> pdb=" O TRP C 91 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE C 115 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 147 Processing helix chain 'C' and resid 148 through 151 removed outlier: 3.978A pdb=" N CYS C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 151' Processing helix chain 'C' and resid 157 through 165 Processing helix chain 'C' and resid 166 through 183 Processing helix chain 'C' and resid 196 through 211 removed outlier: 3.666A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 115 removed outlier: 4.154A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 147 Processing helix chain 'D' and resid 148 through 151 removed outlier: 3.978A pdb=" N CYS D 151 " --> pdb=" O ALA D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 151' Processing helix chain 'D' and resid 157 through 165 Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.667A pdb=" N MET D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET D 211 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 removed outlier: 3.645A pdb=" N THR D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 306 removed outlier: 3.806A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 329 removed outlier: 3.826A pdb=" N GLY D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.36 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1184 1.31 - 1.43: 2633 1.43 - 1.56: 4579 1.56 - 1.68: 0 1.68 - 1.81: 52 Bond restraints: 8448 Sorted by residual: bond pdb=" C12 GB9 D 801 " pdb=" N2 GB9 D 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C12 GB9 C 801 " pdb=" N2 GB9 C 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 B 801 " pdb=" N2 GB9 B 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C12 GB9 A 801 " pdb=" N2 GB9 A 801 " ideal model delta sigma weight residual 1.306 1.481 -0.175 2.00e-02 2.50e+03 7.62e+01 bond pdb=" C5 GB9 C 801 " pdb=" C8 GB9 C 801 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10693 1.35 - 2.70: 593 2.70 - 4.04: 112 4.04 - 5.39: 29 5.39 - 6.74: 9 Bond angle restraints: 11436 Sorted by residual: angle pdb=" N ASN D 258 " pdb=" CA ASN D 258 " pdb=" C ASN D 258 " ideal model delta sigma weight residual 109.07 114.91 -5.84 1.61e+00 3.86e-01 1.32e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N ASN B 258 " pdb=" CA ASN B 258 " pdb=" C ASN B 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N ASN C 258 " pdb=" CA ASN C 258 " pdb=" C ASN C 258 " ideal model delta sigma weight residual 109.07 114.86 -5.79 1.61e+00 3.86e-01 1.29e+01 angle pdb=" N GLU C 257 " pdb=" CA GLU C 257 " pdb=" C GLU C 257 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 ... (remaining 11431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4188 17.35 - 34.69: 456 34.69 - 52.04: 92 52.04 - 69.38: 20 69.38 - 86.73: 16 Dihedral angle restraints: 4772 sinusoidal: 1876 harmonic: 2896 Sorted by residual: dihedral pdb=" CA ARG D 153 " pdb=" C ARG D 153 " pdb=" N TYR D 154 " pdb=" CA TYR D 154 " ideal model delta harmonic sigma weight residual -180.00 -162.79 -17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG A 153 " pdb=" C ARG A 153 " pdb=" N TYR A 154 " pdb=" CA TYR A 154 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 153 " pdb=" C ARG B 153 " pdb=" N TYR B 154 " pdb=" CA TYR B 154 " ideal model delta harmonic sigma weight residual -180.00 -162.83 -17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 658 0.030 - 0.060: 397 0.060 - 0.090: 151 0.090 - 0.120: 24 0.120 - 0.150: 18 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA GLU C 254 " pdb=" N GLU C 254 " pdb=" C GLU C 254 " pdb=" CB GLU C 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA GLU D 254 " pdb=" N GLU D 254 " pdb=" C GLU D 254 " pdb=" CB GLU D 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA GLU B 254 " pdb=" N GLU B 254 " pdb=" C GLU B 254 " pdb=" CB GLU B 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1245 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 284 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO D 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 284 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO C 285 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 284 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO A 285 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.018 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 974 2.73 - 3.27: 8897 3.27 - 3.81: 13274 3.81 - 4.36: 15434 4.36 - 4.90: 26126 Nonbonded interactions: 64705 Sorted by model distance: nonbonded pdb=" O THR B 276 " pdb=" OG1 THR B 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR A 276 " pdb=" OG1 THR A 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR C 276 " pdb=" OG1 THR C 277 " model vdw 2.185 3.040 nonbonded pdb=" O THR D 276 " pdb=" OG1 THR D 277 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLU C 254 " pdb=" N GLN C 286 " model vdw 2.202 3.120 ... (remaining 64700 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.012 0.175 8448 Z= 0.581 Angle : 0.735 6.741 11436 Z= 0.413 Chirality : 0.043 0.150 1248 Planarity : 0.003 0.033 1384 Dihedral : 14.924 86.731 2924 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % 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: -2.00 (0.24), residues: 984 helix: -0.93 (0.15), residues: 808 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.012 0.002 TYR B 154 PHE 0.020 0.002 PHE C 142 TRP 0.013 0.002 TRP C 269 HIS 0.002 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.01235 ( 8448) covalent geometry : angle 0.73451 (11436) hydrogen bonds : bond 0.14436 ( 625) hydrogen bonds : angle 7.20887 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.301 Fit side-chains REVERT: A 76 LYS cc_start: 0.6962 (ptmt) cc_final: 0.6505 (ptmm) REVERT: A 204 GLN cc_start: 0.8762 (mm110) cc_final: 0.8499 (mm110) REVERT: B 76 LYS cc_start: 0.6951 (ptmt) cc_final: 0.6472 (ptmm) REVERT: B 204 GLN cc_start: 0.8758 (mm110) cc_final: 0.8481 (mm110) REVERT: C 204 GLN cc_start: 0.8771 (mm110) cc_final: 0.8491 (mm110) REVERT: D 144 ARG cc_start: 0.6476 (mtt-85) cc_final: 0.6274 (mtt-85) REVERT: D 204 GLN cc_start: 0.8764 (mm110) cc_final: 0.8469 (mm110) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1153 time to fit residues: 32.2216 Evaluate side-chains 189 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.205072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.152562 restraints weight = 9546.844| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.06 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8448 Z= 0.163 Angle : 0.581 6.229 11436 Z= 0.303 Chirality : 0.039 0.157 1248 Planarity : 0.004 0.035 1384 Dihedral : 4.127 14.886 1124 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.03 % Allowed : 14.95 % Favored : 83.01 % 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: 0.69 (0.26), residues: 984 helix: 1.17 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -3.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 201 TYR 0.016 0.002 TYR B 74 PHE 0.009 0.001 PHE C 297 TRP 0.012 0.002 TRP D 146 HIS 0.002 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8448) covalent geometry : angle 0.58053 (11436) hydrogen bonds : bond 0.05054 ( 625) hydrogen bonds : angle 4.63132 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.221 Fit side-chains REVERT: B 89 ARG cc_start: 0.6432 (ptp-110) cc_final: 0.5310 (ptt-90) REVERT: B 326 GLN cc_start: 0.6291 (mt0) cc_final: 0.6068 (tt0) REVERT: C 89 ARG cc_start: 0.6345 (ptp-110) cc_final: 0.5277 (ptt-90) REVERT: C 101 LEU cc_start: 0.8631 (mt) cc_final: 0.8388 (tt) REVERT: D 213 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7845 (ttt180) REVERT: D 326 GLN cc_start: 0.6313 (mt0) cc_final: 0.6086 (tt0) outliers start: 17 outliers final: 12 residues processed: 194 average time/residue: 0.1125 time to fit residues: 28.4858 Evaluate side-chains 193 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 118 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 118 TYR Chi-restraints excluded: chain D residue 171 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.0070 chunk 65 optimal weight: 1.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.205240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.152845 restraints weight = 9583.087| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.19 r_work: 0.3261 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8448 Z= 0.141 Angle : 0.531 6.503 11436 Z= 0.279 Chirality : 0.036 0.132 1248 Planarity : 0.004 0.031 1384 Dihedral : 3.849 13.308 1124 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.23 % Allowed : 18.42 % Favored : 78.35 % 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: 1.56 (0.26), residues: 984 helix: 1.85 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -2.98 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.011 0.001 TYR A 74 PHE 0.014 0.001 PHE C 168 TRP 0.011 0.001 TRP D 146 HIS 0.002 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8448) covalent geometry : angle 0.53149 (11436) hydrogen bonds : bond 0.04589 ( 625) hydrogen bonds : angle 4.16803 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.312 Fit side-chains REVERT: A 101 LEU cc_start: 0.8527 (mt) cc_final: 0.8327 (tt) REVERT: A 120 LYS cc_start: 0.8718 (tppt) cc_final: 0.7783 (tmmt) REVERT: A 165 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7166 (ttt-90) REVERT: A 206 LEU cc_start: 0.8318 (mp) cc_final: 0.7728 (mp) REVERT: A 320 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8755 (t) REVERT: B 76 LYS cc_start: 0.7115 (ptmt) cc_final: 0.6662 (ptmm) REVERT: B 78 GLN cc_start: 0.6838 (tm-30) cc_final: 0.6544 (tm-30) REVERT: B 120 LYS cc_start: 0.8730 (tppt) cc_final: 0.7779 (tmmt) REVERT: B 165 ARG cc_start: 0.7331 (ttp80) cc_final: 0.7107 (ttt-90) REVERT: B 206 LEU cc_start: 0.8342 (mp) cc_final: 0.7750 (mp) REVERT: B 320 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8759 (t) REVERT: C 76 LYS cc_start: 0.7069 (ptmt) cc_final: 0.6613 (ptmm) REVERT: C 78 GLN cc_start: 0.6868 (tm-30) cc_final: 0.6577 (tm-30) REVERT: C 86 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6229 (mm-30) REVERT: C 120 LYS cc_start: 0.8699 (tppt) cc_final: 0.7768 (tmmt) REVERT: C 165 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7122 (ttt-90) REVERT: C 206 LEU cc_start: 0.8312 (mp) cc_final: 0.7731 (mp) REVERT: C 213 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7816 (ttt180) REVERT: C 320 VAL cc_start: 0.9020 (OUTLIER) cc_final: 0.8792 (t) REVERT: D 76 LYS cc_start: 0.7083 (ptmt) cc_final: 0.6637 (ptmm) REVERT: D 78 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6618 (tm-30) REVERT: D 101 LEU cc_start: 0.8526 (mt) cc_final: 0.8316 (tt) REVERT: D 120 LYS cc_start: 0.8709 (tppt) cc_final: 0.7762 (tmmt) REVERT: D 165 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7062 (ttp80) REVERT: D 171 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7022 (tt) REVERT: D 206 LEU cc_start: 0.8318 (mp) cc_final: 0.7746 (mp) REVERT: D 320 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8762 (t) outliers start: 27 outliers final: 16 residues processed: 201 average time/residue: 0.1089 time to fit residues: 28.6115 Evaluate side-chains 190 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.199824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.159326 restraints weight = 9612.223| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.43 r_work: 0.3204 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8448 Z= 0.139 Angle : 0.516 6.266 11436 Z= 0.268 Chirality : 0.036 0.137 1248 Planarity : 0.003 0.033 1384 Dihedral : 3.725 12.565 1124 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % Favored : 77.27 % 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: 2.08 (0.27), residues: 984 helix: 2.17 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.73 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 144 TYR 0.010 0.001 TYR A 284 PHE 0.018 0.001 PHE D 168 TRP 0.011 0.001 TRP D 146 HIS 0.002 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8448) covalent geometry : angle 0.51591 (11436) hydrogen bonds : bond 0.04411 ( 625) hydrogen bonds : angle 3.91985 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.308 Fit side-chains REVERT: A 76 LYS cc_start: 0.7207 (ptmt) cc_final: 0.6733 (ptmm) REVERT: A 86 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6470 (mm-30) REVERT: A 101 LEU cc_start: 0.8530 (mt) cc_final: 0.8191 (tt) REVERT: A 120 LYS cc_start: 0.8718 (tppt) cc_final: 0.7835 (tmmt) REVERT: A 127 TYR cc_start: 0.6847 (t80) cc_final: 0.6103 (m-80) REVERT: A 206 LEU cc_start: 0.8371 (mp) cc_final: 0.7787 (mp) REVERT: A 213 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7610 (ttt180) REVERT: A 320 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8804 (t) REVERT: B 76 LYS cc_start: 0.7210 (ptmt) cc_final: 0.6718 (ptmm) REVERT: B 78 GLN cc_start: 0.7063 (tm-30) cc_final: 0.6695 (tm-30) REVERT: B 86 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6517 (mm-30) REVERT: B 120 LYS cc_start: 0.8701 (tppt) cc_final: 0.7819 (tmmt) REVERT: B 127 TYR cc_start: 0.6831 (t80) cc_final: 0.6096 (m-80) REVERT: B 158 ARG cc_start: 0.6391 (tpt170) cc_final: 0.6109 (mtp85) REVERT: B 165 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7237 (ttt-90) REVERT: B 206 LEU cc_start: 0.8389 (mp) cc_final: 0.7805 (mp) REVERT: B 213 ARG cc_start: 0.7901 (ttt180) cc_final: 0.7593 (ttt180) REVERT: B 320 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (t) REVERT: C 76 LYS cc_start: 0.7180 (ptmt) cc_final: 0.6706 (ptmm) REVERT: C 78 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6687 (tm-30) REVERT: C 120 LYS cc_start: 0.8704 (tppt) cc_final: 0.7838 (tmmt) REVERT: C 127 TYR cc_start: 0.6725 (t80) cc_final: 0.6089 (m-80) REVERT: C 165 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7137 (ttt-90) REVERT: C 206 LEU cc_start: 0.8385 (mp) cc_final: 0.7807 (mp) REVERT: C 213 ARG cc_start: 0.7905 (ttt180) cc_final: 0.7695 (ttt180) REVERT: C 320 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8773 (t) REVERT: D 76 LYS cc_start: 0.7192 (ptmt) cc_final: 0.6716 (ptmm) REVERT: D 78 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6669 (tm-30) REVERT: D 101 LEU cc_start: 0.8550 (mt) cc_final: 0.8197 (tt) REVERT: D 120 LYS cc_start: 0.8699 (tppt) cc_final: 0.7820 (tmmt) REVERT: D 127 TYR cc_start: 0.6811 (t80) cc_final: 0.6102 (m-80) REVERT: D 165 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7191 (ttt-90) REVERT: D 206 LEU cc_start: 0.8376 (mp) cc_final: 0.7776 (mp) REVERT: D 320 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8718 (t) outliers start: 38 outliers final: 19 residues processed: 198 average time/residue: 0.1037 time to fit residues: 27.3320 Evaluate side-chains 188 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 89 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 96 HIS B 204 GLN C 96 HIS C 204 GLN D 96 HIS D 204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.207843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.156206 restraints weight = 9597.006| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.20 r_work: 0.3307 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8448 Z= 0.115 Angle : 0.483 5.246 11436 Z= 0.249 Chirality : 0.034 0.120 1248 Planarity : 0.003 0.030 1384 Dihedral : 3.647 13.568 1124 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.11 % Allowed : 19.98 % Favored : 76.91 % 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: 2.58 (0.27), residues: 984 helix: 2.50 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.44 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.009 0.001 TYR D 284 PHE 0.012 0.001 PHE D 168 TRP 0.013 0.001 TRP A 146 HIS 0.002 0.000 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8448) covalent geometry : angle 0.48268 (11436) hydrogen bonds : bond 0.03972 ( 625) hydrogen bonds : angle 3.69089 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.299 Fit side-chains REVERT: A 76 LYS cc_start: 0.7232 (ptmt) cc_final: 0.6792 (ptmm) REVERT: A 101 LEU cc_start: 0.8515 (mt) cc_final: 0.8236 (tt) REVERT: A 120 LYS cc_start: 0.8760 (tppt) cc_final: 0.7825 (tmmt) REVERT: A 127 TYR cc_start: 0.6885 (t80) cc_final: 0.6073 (m-80) REVERT: A 206 LEU cc_start: 0.8334 (mp) cc_final: 0.7796 (mp) REVERT: A 320 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8826 (t) REVERT: B 76 LYS cc_start: 0.7222 (ptmt) cc_final: 0.6856 (pttt) REVERT: B 78 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 120 LYS cc_start: 0.8727 (tppt) cc_final: 0.7816 (tmmt) REVERT: B 127 TYR cc_start: 0.6805 (t80) cc_final: 0.6004 (m-80) REVERT: B 158 ARG cc_start: 0.6343 (tpt170) cc_final: 0.6069 (mtp85) REVERT: B 165 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7244 (ttt-90) REVERT: B 206 LEU cc_start: 0.8319 (mp) cc_final: 0.7776 (mp) REVERT: B 213 ARG cc_start: 0.8037 (ttt180) cc_final: 0.7746 (ttt180) REVERT: C 76 LYS cc_start: 0.7191 (ptmt) cc_final: 0.6733 (ptmm) REVERT: C 78 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 120 LYS cc_start: 0.8693 (tppt) cc_final: 0.7795 (tmmt) REVERT: C 127 TYR cc_start: 0.6838 (t80) cc_final: 0.6082 (m-80) REVERT: C 165 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7227 (ttt-90) REVERT: C 171 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7097 (tt) REVERT: C 206 LEU cc_start: 0.8298 (mp) cc_final: 0.7770 (mp) REVERT: D 76 LYS cc_start: 0.7216 (ptmt) cc_final: 0.6836 (pttt) REVERT: D 78 GLN cc_start: 0.6960 (tm-30) cc_final: 0.6654 (tm-30) REVERT: D 101 LEU cc_start: 0.8506 (mt) cc_final: 0.8215 (tt) REVERT: D 120 LYS cc_start: 0.8709 (tppt) cc_final: 0.7788 (tmmt) REVERT: D 127 TYR cc_start: 0.6915 (t80) cc_final: 0.6102 (m-80) REVERT: D 165 ARG cc_start: 0.7460 (ttp80) cc_final: 0.7139 (ttp80) REVERT: D 171 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.7034 (tt) REVERT: D 206 LEU cc_start: 0.8325 (mp) cc_final: 0.7786 (mp) REVERT: D 320 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8718 (t) outliers start: 26 outliers final: 13 residues processed: 184 average time/residue: 0.0996 time to fit residues: 24.4258 Evaluate side-chains 185 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.206708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156663 restraints weight = 9505.719| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.67 r_work: 0.3201 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8448 Z= 0.133 Angle : 0.490 7.222 11436 Z= 0.253 Chirality : 0.035 0.126 1248 Planarity : 0.003 0.031 1384 Dihedral : 3.598 13.658 1124 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.75 % Allowed : 19.86 % Favored : 77.39 % 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: 2.75 (0.27), residues: 984 helix: 2.58 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.20 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.010 0.001 TYR D 284 PHE 0.011 0.001 PHE D 168 TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8448) covalent geometry : angle 0.48966 (11436) hydrogen bonds : bond 0.04187 ( 625) hydrogen bonds : angle 3.64609 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.264 Fit side-chains REVERT: A 76 LYS cc_start: 0.7352 (ptmt) cc_final: 0.6862 (ptmm) REVERT: A 86 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6883 (mm-30) REVERT: A 120 LYS cc_start: 0.8753 (tppt) cc_final: 0.7823 (tmmt) REVERT: A 127 TYR cc_start: 0.6899 (t80) cc_final: 0.6116 (m-80) REVERT: A 206 LEU cc_start: 0.8376 (mp) cc_final: 0.7818 (mp) REVERT: A 249 LEU cc_start: 0.9291 (mm) cc_final: 0.9047 (mm) REVERT: B 76 LYS cc_start: 0.7392 (ptmt) cc_final: 0.7008 (pttt) REVERT: B 78 GLN cc_start: 0.7086 (tm-30) cc_final: 0.6737 (tm-30) REVERT: B 86 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6639 (mm-30) REVERT: B 120 LYS cc_start: 0.8702 (tppt) cc_final: 0.7809 (tmmt) REVERT: B 127 TYR cc_start: 0.6975 (t80) cc_final: 0.6122 (m-80) REVERT: B 158 ARG cc_start: 0.6466 (tpt170) cc_final: 0.6207 (mtp85) REVERT: B 206 LEU cc_start: 0.8394 (mp) cc_final: 0.7846 (mp) REVERT: B 249 LEU cc_start: 0.9283 (mm) cc_final: 0.9030 (mm) REVERT: C 76 LYS cc_start: 0.7275 (ptmt) cc_final: 0.6880 (pttt) REVERT: C 78 GLN cc_start: 0.7067 (tm-30) cc_final: 0.6737 (tm-30) REVERT: C 86 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6688 (mm-30) REVERT: C 120 LYS cc_start: 0.8701 (tppt) cc_final: 0.7819 (tmmt) REVERT: C 127 TYR cc_start: 0.6792 (t80) cc_final: 0.6071 (m-80) REVERT: C 165 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7211 (ttt-90) REVERT: C 206 LEU cc_start: 0.8353 (mp) cc_final: 0.7792 (mp) REVERT: C 213 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7538 (ttt180) REVERT: D 76 LYS cc_start: 0.7305 (ptmt) cc_final: 0.6901 (pttt) REVERT: D 78 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6694 (tm-30) REVERT: D 101 LEU cc_start: 0.8549 (mt) cc_final: 0.8253 (tt) REVERT: D 120 LYS cc_start: 0.8704 (tppt) cc_final: 0.7802 (tmmt) REVERT: D 127 TYR cc_start: 0.6903 (t80) cc_final: 0.6122 (m-80) REVERT: D 206 LEU cc_start: 0.8343 (mp) cc_final: 0.7791 (mp) REVERT: D 320 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8700 (t) outliers start: 23 outliers final: 18 residues processed: 182 average time/residue: 0.0927 time to fit residues: 22.7432 Evaluate side-chains 182 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 204 GLN C 204 GLN D 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.208355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.171125 restraints weight = 9468.887| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.22 r_work: 0.3345 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8448 Z= 0.126 Angle : 0.480 6.559 11436 Z= 0.248 Chirality : 0.035 0.121 1248 Planarity : 0.003 0.026 1384 Dihedral : 3.543 14.409 1124 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 19.98 % Favored : 77.51 % 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: 2.88 (0.27), residues: 984 helix: 2.64 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -2.00 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 210 TYR 0.017 0.001 TYR A 82 PHE 0.010 0.001 PHE D 168 TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8448) covalent geometry : angle 0.47990 (11436) hydrogen bonds : bond 0.03981 ( 625) hydrogen bonds : angle 3.59985 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.203 Fit side-chains REVERT: A 76 LYS cc_start: 0.7382 (ptmt) cc_final: 0.7009 (pttt) REVERT: A 86 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6577 (mm-30) REVERT: A 120 LYS cc_start: 0.8702 (tppt) cc_final: 0.7824 (tmmt) REVERT: A 127 TYR cc_start: 0.6801 (t80) cc_final: 0.6104 (m-80) REVERT: A 158 ARG cc_start: 0.6388 (tpt170) cc_final: 0.6067 (mtp85) REVERT: A 206 LEU cc_start: 0.8435 (mp) cc_final: 0.7898 (mp) REVERT: B 76 LYS cc_start: 0.7396 (ptmt) cc_final: 0.7031 (pttt) REVERT: B 78 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6697 (tm-30) REVERT: B 120 LYS cc_start: 0.8663 (tppt) cc_final: 0.7814 (tmmt) REVERT: B 127 TYR cc_start: 0.7048 (t80) cc_final: 0.6169 (m-80) REVERT: B 158 ARG cc_start: 0.6464 (tpt170) cc_final: 0.6262 (mtp85) REVERT: B 206 LEU cc_start: 0.8432 (mp) cc_final: 0.7912 (mp) REVERT: C 76 LYS cc_start: 0.7316 (ptmt) cc_final: 0.6919 (pttt) REVERT: C 78 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6703 (tm-30) REVERT: C 86 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6641 (mm-30) REVERT: C 120 LYS cc_start: 0.8662 (tppt) cc_final: 0.7782 (tmmt) REVERT: C 127 TYR cc_start: 0.7046 (t80) cc_final: 0.6203 (m-80) REVERT: C 158 ARG cc_start: 0.6483 (tpt170) cc_final: 0.6160 (mtp85) REVERT: C 206 LEU cc_start: 0.8388 (mp) cc_final: 0.7850 (mp) REVERT: C 213 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7485 (ttt180) REVERT: D 76 LYS cc_start: 0.7335 (ptmt) cc_final: 0.6928 (pttt) REVERT: D 78 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6680 (tm-30) REVERT: D 120 LYS cc_start: 0.8676 (tppt) cc_final: 0.7779 (tmmt) REVERT: D 127 TYR cc_start: 0.6874 (t80) cc_final: 0.6125 (m-80) REVERT: D 206 LEU cc_start: 0.8359 (mp) cc_final: 0.7828 (mp) REVERT: D 209 ILE cc_start: 0.8761 (mp) cc_final: 0.8430 (tt) outliers start: 21 outliers final: 15 residues processed: 177 average time/residue: 0.1027 time to fit residues: 24.2786 Evaluate side-chains 176 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.201650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.156699 restraints weight = 9350.478| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.31 r_work: 0.3224 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8448 Z= 0.145 Angle : 0.520 6.326 11436 Z= 0.266 Chirality : 0.036 0.146 1248 Planarity : 0.003 0.052 1384 Dihedral : 3.548 13.603 1124 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 19.98 % Favored : 77.51 % 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: 2.89 (0.27), residues: 984 helix: 2.65 (0.17), residues: 812 sheet: None (None), residues: 0 loop : -1.97 (0.52), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 213 TYR 0.015 0.001 TYR A 82 PHE 0.015 0.001 PHE B 168 TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8448) covalent geometry : angle 0.52005 (11436) hydrogen bonds : bond 0.04211 ( 625) hydrogen bonds : angle 3.64069 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.326 Fit side-chains REVERT: A 76 LYS cc_start: 0.7358 (ptmt) cc_final: 0.6995 (pttt) REVERT: A 120 LYS cc_start: 0.8693 (tppt) cc_final: 0.7797 (tmmt) REVERT: A 127 TYR cc_start: 0.6835 (t80) cc_final: 0.6131 (m-80) REVERT: A 158 ARG cc_start: 0.6317 (tpt170) cc_final: 0.5995 (mtp85) REVERT: A 206 LEU cc_start: 0.8320 (mp) cc_final: 0.7815 (mp) REVERT: B 76 LYS cc_start: 0.7328 (ptmt) cc_final: 0.6983 (pttt) REVERT: B 78 GLN cc_start: 0.6896 (tm-30) cc_final: 0.6626 (tm-30) REVERT: B 120 LYS cc_start: 0.8651 (tppt) cc_final: 0.7791 (tmmt) REVERT: B 127 TYR cc_start: 0.7029 (t80) cc_final: 0.6176 (m-80) REVERT: B 158 ARG cc_start: 0.6380 (tpt170) cc_final: 0.6147 (mtp85) REVERT: B 206 LEU cc_start: 0.8334 (mp) cc_final: 0.7838 (mp) REVERT: C 76 LYS cc_start: 0.7271 (ptmt) cc_final: 0.6912 (pttt) REVERT: C 78 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6599 (tm-30) REVERT: C 86 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6609 (mm-30) REVERT: C 120 LYS cc_start: 0.8657 (tppt) cc_final: 0.7815 (tmmt) REVERT: C 127 TYR cc_start: 0.7017 (t80) cc_final: 0.6184 (m-80) REVERT: C 158 ARG cc_start: 0.6387 (tpt170) cc_final: 0.6055 (mtp85) REVERT: C 206 LEU cc_start: 0.8278 (mp) cc_final: 0.7780 (mp) REVERT: C 213 ARG cc_start: 0.7836 (ttt180) cc_final: 0.7540 (ttt180) REVERT: D 76 LYS cc_start: 0.7230 (ptmt) cc_final: 0.6897 (pttt) REVERT: D 78 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6537 (tm-30) REVERT: D 120 LYS cc_start: 0.8650 (tppt) cc_final: 0.7761 (tmmt) REVERT: D 127 TYR cc_start: 0.6898 (t80) cc_final: 0.6142 (m-80) REVERT: D 206 LEU cc_start: 0.8262 (mp) cc_final: 0.7738 (mp) REVERT: D 209 ILE cc_start: 0.8620 (mp) cc_final: 0.8360 (tt) outliers start: 21 outliers final: 19 residues processed: 188 average time/residue: 0.0880 time to fit residues: 22.4357 Evaluate side-chains 183 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.207877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.166274 restraints weight = 9418.329| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.31 r_work: 0.3303 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8448 Z= 0.132 Angle : 0.537 10.493 11436 Z= 0.268 Chirality : 0.040 0.360 1248 Planarity : 0.003 0.039 1384 Dihedral : 3.540 13.738 1124 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.23 % Allowed : 19.62 % Favored : 77.15 % 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: 2.84 (0.27), residues: 984 helix: 2.59 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 213 TYR 0.015 0.001 TYR A 82 PHE 0.022 0.001 PHE D 137 TRP 0.015 0.001 TRP A 146 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8448) covalent geometry : angle 0.53742 (11436) hydrogen bonds : bond 0.04113 ( 625) hydrogen bonds : angle 3.64872 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.266 Fit side-chains REVERT: A 76 LYS cc_start: 0.7471 (ptmt) cc_final: 0.7119 (pttt) REVERT: A 120 LYS cc_start: 0.8703 (tppt) cc_final: 0.7790 (tmmt) REVERT: A 127 TYR cc_start: 0.6802 (t80) cc_final: 0.6093 (m-80) REVERT: A 158 ARG cc_start: 0.6409 (tpt170) cc_final: 0.6112 (mtp85) REVERT: A 206 LEU cc_start: 0.8391 (mp) cc_final: 0.7890 (mp) REVERT: B 76 LYS cc_start: 0.7382 (ptmt) cc_final: 0.6987 (pttt) REVERT: B 78 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6648 (tm-30) REVERT: B 120 LYS cc_start: 0.8666 (tppt) cc_final: 0.7795 (tmmt) REVERT: B 127 TYR cc_start: 0.7076 (t80) cc_final: 0.6190 (m-80) REVERT: B 158 ARG cc_start: 0.6397 (tpt170) cc_final: 0.6181 (mtp85) REVERT: B 206 LEU cc_start: 0.8410 (mp) cc_final: 0.7899 (mp) REVERT: C 76 LYS cc_start: 0.7351 (ptmt) cc_final: 0.6951 (pttt) REVERT: C 78 GLN cc_start: 0.7004 (tm-30) cc_final: 0.6679 (tm-30) REVERT: C 86 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6707 (mm-30) REVERT: C 93 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6627 (t80) REVERT: C 120 LYS cc_start: 0.8660 (tppt) cc_final: 0.7813 (tmmt) REVERT: C 127 TYR cc_start: 0.7017 (t80) cc_final: 0.6171 (m-80) REVERT: C 158 ARG cc_start: 0.6397 (tpt170) cc_final: 0.6078 (mtp85) REVERT: C 206 LEU cc_start: 0.8376 (mp) cc_final: 0.7864 (mp) REVERT: C 213 ARG cc_start: 0.7838 (ttt180) cc_final: 0.7549 (ttt180) REVERT: D 76 LYS cc_start: 0.7388 (ptmt) cc_final: 0.7001 (pttt) REVERT: D 78 GLN cc_start: 0.6989 (tm-30) cc_final: 0.6657 (tm-30) REVERT: D 93 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6608 (t80) REVERT: D 120 LYS cc_start: 0.8676 (tppt) cc_final: 0.7769 (tmmt) REVERT: D 127 TYR cc_start: 0.6944 (t80) cc_final: 0.6145 (m-80) REVERT: D 206 LEU cc_start: 0.8295 (mp) cc_final: 0.7754 (mp) outliers start: 27 outliers final: 22 residues processed: 184 average time/residue: 0.0853 time to fit residues: 21.3809 Evaluate side-chains 187 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.207693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.164782 restraints weight = 9404.684| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.16 r_work: 0.3307 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8448 Z= 0.141 Angle : 0.539 10.018 11436 Z= 0.272 Chirality : 0.040 0.352 1248 Planarity : 0.003 0.030 1384 Dihedral : 3.516 12.823 1124 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.99 % Allowed : 19.50 % Favored : 77.51 % 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: 2.82 (0.27), residues: 984 helix: 2.57 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.72 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.018 0.001 TYR C 82 PHE 0.026 0.001 PHE B 316 TRP 0.016 0.001 TRP D 146 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8448) covalent geometry : angle 0.53892 (11436) hydrogen bonds : bond 0.04228 ( 625) hydrogen bonds : angle 3.66615 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.312 Fit side-chains REVERT: A 76 LYS cc_start: 0.7359 (ptmt) cc_final: 0.7031 (pttt) REVERT: A 120 LYS cc_start: 0.8684 (tppt) cc_final: 0.7787 (tmmt) REVERT: A 127 TYR cc_start: 0.6746 (t80) cc_final: 0.6057 (m-80) REVERT: A 158 ARG cc_start: 0.6415 (tpt170) cc_final: 0.6124 (mtp85) REVERT: A 206 LEU cc_start: 0.8396 (mp) cc_final: 0.7894 (mp) REVERT: B 76 LYS cc_start: 0.7297 (ptmt) cc_final: 0.6916 (pttt) REVERT: B 78 GLN cc_start: 0.7028 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 120 LYS cc_start: 0.8649 (tppt) cc_final: 0.7808 (tmmt) REVERT: B 127 TYR cc_start: 0.7045 (t80) cc_final: 0.6202 (m-80) REVERT: B 158 ARG cc_start: 0.6406 (tpt170) cc_final: 0.6192 (mtp85) REVERT: B 206 LEU cc_start: 0.8414 (mp) cc_final: 0.7897 (mp) REVERT: C 76 LYS cc_start: 0.7399 (ptmt) cc_final: 0.7006 (pttt) REVERT: C 78 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6674 (tm-30) REVERT: C 86 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6872 (mm-30) REVERT: C 93 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6686 (t80) REVERT: C 120 LYS cc_start: 0.8668 (tppt) cc_final: 0.7836 (tmmt) REVERT: C 127 TYR cc_start: 0.7161 (t80) cc_final: 0.6257 (m-80) REVERT: C 158 ARG cc_start: 0.6435 (tpt170) cc_final: 0.6117 (mtp85) REVERT: C 206 LEU cc_start: 0.8377 (mp) cc_final: 0.7874 (mp) REVERT: C 213 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7468 (ttt180) REVERT: D 76 LYS cc_start: 0.7409 (ptmt) cc_final: 0.7027 (pttt) REVERT: D 78 GLN cc_start: 0.6999 (tm-30) cc_final: 0.6674 (tm-30) REVERT: D 93 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6603 (t80) REVERT: D 120 LYS cc_start: 0.8644 (tppt) cc_final: 0.7771 (tmmt) REVERT: D 127 TYR cc_start: 0.7017 (t80) cc_final: 0.6117 (m-80) REVERT: D 206 LEU cc_start: 0.8231 (mp) cc_final: 0.7916 (mp) outliers start: 25 outliers final: 22 residues processed: 186 average time/residue: 0.0883 time to fit residues: 22.4042 Evaluate side-chains 190 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 95 TYR Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 93 PHE Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.208070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.164483 restraints weight = 9432.140| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.19 r_work: 0.3307 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8448 Z= 0.136 Angle : 0.529 9.585 11436 Z= 0.266 Chirality : 0.039 0.338 1248 Planarity : 0.003 0.040 1384 Dihedral : 3.493 12.735 1124 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.11 % Allowed : 19.98 % Favored : 76.91 % 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: 2.87 (0.27), residues: 984 helix: 2.61 (0.17), residues: 808 sheet: None (None), residues: 0 loop : -1.71 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.017 0.001 TYR C 82 PHE 0.025 0.001 PHE B 316 TRP 0.015 0.001 TRP A 146 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8448) covalent geometry : angle 0.52888 (11436) hydrogen bonds : bond 0.04152 ( 625) hydrogen bonds : angle 3.63584 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.55 seconds wall clock time: 35 minutes 14.64 seconds (2114.64 seconds total)