Starting phenix.real_space_refine on Tue Aug 4 21:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdd_45468/08_2026/9cdd_45468_neut.cif" } resolution = 3.05 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= 0.014 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 12 5.49 5 S 57 5.16 5 C 4761 2.51 5 N 903 2.21 5 O 1134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6867 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1954 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 335 Unusual residues: {'CLR': 3, 'PEE': 4, 'RET': 1} Classifications: {'undetermined': 8, 'water': 27} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Restraints were copied for chains: B, C Time building chain proxies: 1.58, per 1000 atoms: 0.23 Number of scatterers: 6867 At special positions: 0 Unit cell: (76.22, 79.31, 76.22, 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 57 16.00 P 12 15.00 O 1134 8.00 N 903 7.00 C 4761 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 373.6 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 76.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.515A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.514A pdb=" N ILE B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 167 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG B 176 " --> pdb=" O HIS B 172 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.515A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.538A pdb=" N CYS C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 167 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 168 through 178 removed outlier: 3.605A pdb=" N ARG C 176 " --> pdb=" O HIS C 172 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.270A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.745A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 removed outlier: 4.002A pdb=" N TYR C 222 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 372 hydrogen bonds defined for protein. 1116 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: 1.00 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1145 1.33 - 1.45: 1858 1.45 - 1.57: 3873 1.57 - 1.69: 60 1.69 - 1.81: 90 Bond restraints: 7026 Sorted by residual: bond pdb=" O4P PEE A 305 " pdb=" P PEE A 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE C 305 " pdb=" P PEE C 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O4P PEE B 305 " pdb=" P PEE B 305 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" O4P PEE B 306 " pdb=" P PEE B 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O4P PEE A 306 " pdb=" P PEE A 306 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 7021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 9078 2.79 - 5.58: 288 5.58 - 8.37: 81 8.37 - 11.16: 6 11.16 - 13.95: 12 Bond angle restraints: 9465 Sorted by residual: angle pdb=" O1P PEE A 305 " pdb=" P PEE A 305 " pdb=" O2P PEE A 305 " ideal model delta sigma weight residual 119.43 133.38 -13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE C 305 " pdb=" P PEE C 305 " pdb=" O2P PEE C 305 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE B 305 " pdb=" P PEE B 305 " pdb=" O2P PEE B 305 " ideal model delta sigma weight residual 119.43 133.37 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" O1P PEE A 306 " pdb=" P PEE A 306 " pdb=" O2P PEE A 306 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE C 306 " pdb=" P PEE C 306 " pdb=" O2P PEE C 306 " ideal model delta sigma weight residual 119.43 133.24 -13.81 3.00e+00 1.11e-01 2.12e+01 ... (remaining 9460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 4236 34.47 - 68.95: 234 68.95 - 103.42: 27 103.42 - 137.90: 15 137.90 - 172.37: 33 Dihedral angle restraints: 4545 sinusoidal: 2451 harmonic: 2094 Sorted by residual: dihedral pdb=" N PEE C 305 " pdb=" C4 PEE C 305 " pdb=" C5 PEE C 305 " pdb=" O4P PEE C 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.40 -172.37 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE B 305 " pdb=" C4 PEE B 305 " pdb=" C5 PEE B 305 " pdb=" O4P PEE B 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.39 -172.36 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PEE A 305 " pdb=" C4 PEE A 305 " pdb=" C5 PEE A 305 " pdb=" O4P PEE A 305 " ideal model delta sinusoidal sigma weight residual -56.97 115.39 -172.36 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 859 0.086 - 0.172: 47 0.172 - 0.258: 15 0.258 - 0.344: 18 0.344 - 0.430: 18 Chirality restraints: 957 Sorted by residual: chirality pdb=" C2 PEE A 305 " pdb=" C1 PEE A 305 " pdb=" C3 PEE A 305 " pdb=" O2 PEE A 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" C2 PEE C 305 " pdb=" C1 PEE C 305 " pdb=" C3 PEE C 305 " pdb=" O2 PEE C 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2 PEE B 305 " pdb=" C1 PEE B 305 " pdb=" C3 PEE B 305 " pdb=" O2 PEE B 305 " both_signs ideal model delta sigma weight residual False -2.33 -2.76 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 954 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 RET B 301 " 0.045 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C7 RET B 301 " -0.043 2.00e-02 2.50e+03 pdb=" C8 RET B 301 " -0.049 2.00e-02 2.50e+03 pdb=" C9 RET B 301 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 RET A 301 " -0.045 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C7 RET A 301 " 0.043 2.00e-02 2.50e+03 pdb=" C8 RET A 301 " 0.049 2.00e-02 2.50e+03 pdb=" C9 RET A 301 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 RET C 301 " 0.045 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C7 RET C 301 " -0.042 2.00e-02 2.50e+03 pdb=" C8 RET C 301 " -0.049 2.00e-02 2.50e+03 pdb=" C9 RET C 301 " 0.046 2.00e-02 2.50e+03 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 0.63 - 1.48: 21 1.48 - 2.34: 51 2.34 - 3.19: 6391 3.19 - 4.05: 18560 4.05 - 4.90: 36464 Warning: very small nonbonded interaction distances. Nonbonded interactions: 61487 Sorted by model distance: nonbonded pdb=" CZ ARG B 62 " pdb=" CG PRO C 124 " model vdw 0.629 3.670 nonbonded pdb=" CZ ARG A 62 " pdb=" CG PRO B 124 " model vdw 0.631 3.670 nonbonded pdb=" CG PRO A 124 " pdb=" CZ ARG C 62 " model vdw 0.637 3.670 nonbonded pdb=" CA PRO A 124 " pdb=" NH1 ARG C 62 " model vdw 0.731 3.550 nonbonded pdb=" NH1 ARG A 62 " pdb=" CA PRO B 124 " model vdw 0.735 3.550 ... (remaining 61482 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' } 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: 1.190 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: 7.750 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 : 0.014 0.478 7032 Z= 1.102 Angle : 1.210 13.948 9465 Z= 0.463 Chirality : 0.085 0.430 957 Planarity : 0.005 0.046 1044 Dihedral : 25.461 172.369 3213 Min Nonbonded Distance : 0.629 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 9.27 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.31), residues: 714 helix: 0.03 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 151 TYR 0.012 0.002 TYR B 103 PHE 0.019 0.002 PHE B 195 TRP 0.009 0.002 TRP B 190 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.46 ( 7026) covalent geometry : angle 1.20987 / 0.46 ( 9465) hydrogen bonds : bond 0.25592 / 17.61 ( 372) hydrogen bonds : angle 7.46603 / 5.20 ( 1116) Misc. bond : bond 0.34311 / 16.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.3217 (mtt) cc_final: 0.2998 (mtm) REVERT: A 172 HIS cc_start: 0.7177 (m170) cc_final: 0.6875 (m-70) REVERT: A 187 TRP cc_start: 0.7171 (m100) cc_final: 0.6953 (m100) REVERT: B 51 MET cc_start: 0.4492 (mtt) cc_final: 0.3728 (ttp) REVERT: B 235 ILE cc_start: 0.7388 (mt) cc_final: 0.7089 (mt) REVERT: C 35 PHE cc_start: 0.7394 (t80) cc_final: 0.6479 (t80) REVERT: C 134 PHE cc_start: 0.7570 (t80) cc_final: 0.7313 (t80) REVERT: C 186 ARG cc_start: 0.5362 (ttp-110) cc_final: 0.4960 (ttp80) REVERT: C 234 SER cc_start: 0.8013 (p) cc_final: 0.7488 (m) outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.0802 time to fit residues: 20.1317 Evaluate side-chains 143 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN ** C 225 HIS ** 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 = 0.4259 r_free = 0.4259 target = 0.195831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.171483 restraints weight = 6822.127| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.42 r_work: 0.3858 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7032 Z= 0.165 Angle : 0.650 8.816 9465 Z= 0.313 Chirality : 0.040 0.127 957 Planarity : 0.005 0.043 1044 Dihedral : 26.175 176.946 1964 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.93 % Allowed : 11.22 % Favored : 85.85 % 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: 0.11 (0.31), residues: 714 helix: 0.68 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.31 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 62 TYR 0.032 0.002 TYR C 81 PHE 0.022 0.002 PHE B 195 TRP 0.013 0.002 TRP A 190 HIS 0.011 0.003 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7026) covalent geometry : angle 0.64968 / 0.31 ( 9465) hydrogen bonds : bond 0.04928 / 3.26 ( 372) hydrogen bonds : angle 4.85983 / 3.46 ( 1116) Misc. bond : bond 0.00020 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.7362 (t80) cc_final: 0.7156 (t80) REVERT: B 47 LEU cc_start: 0.7861 (tp) cc_final: 0.7610 (tp) REVERT: B 51 MET cc_start: 0.4334 (mtt) cc_final: 0.3825 (ttm) REVERT: B 81 TYR cc_start: 0.6775 (m-80) cc_final: 0.5967 (m-80) REVERT: B 171 ARG cc_start: 0.6441 (mtm110) cc_final: 0.5876 (mtm110) REVERT: B 218 GLN cc_start: 0.5036 (tt0) cc_final: 0.3886 (tp-100) outliers start: 18 outliers final: 9 residues processed: 159 average time/residue: 0.0771 time to fit residues: 16.9509 Evaluate side-chains 127 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 217 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168971 restraints weight = 6891.529| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.44 r_work: 0.3840 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7032 Z= 0.144 Angle : 0.601 8.841 9465 Z= 0.293 Chirality : 0.040 0.122 957 Planarity : 0.004 0.038 1044 Dihedral : 23.264 179.416 1954 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.76 % Allowed : 13.66 % Favored : 83.58 % 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: 0.64 (0.31), residues: 714 helix: 1.08 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.14 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 176 TYR 0.030 0.002 TYR C 81 PHE 0.030 0.002 PHE C 134 TRP 0.011 0.001 TRP B 42 HIS 0.004 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7026) covalent geometry : angle 0.60055 / 0.29 ( 9465) hydrogen bonds : bond 0.04485 / 2.97 ( 372) hydrogen bonds : angle 4.58538 / 3.27 ( 1116) Misc. bond : bond 0.00027 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TRP cc_start: 0.6963 (m100) cc_final: 0.6496 (m100) REVERT: A 229 ASP cc_start: 0.7927 (m-30) cc_final: 0.7569 (m-30) REVERT: A 231 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6927 (p) REVERT: B 51 MET cc_start: 0.5134 (mtt) cc_final: 0.4265 (ttm) REVERT: B 105 ASP cc_start: 0.7895 (p0) cc_final: 0.7537 (p0) REVERT: B 174 LYS cc_start: 0.8253 (tttm) cc_final: 0.7460 (mttp) REVERT: C 240 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6401 (mpp) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 0.0648 time to fit residues: 12.7280 Evaluate side-chains 132 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164402 restraints weight = 6846.677| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.41 r_work: 0.3799 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7032 Z= 0.149 Angle : 0.608 7.068 9465 Z= 0.294 Chirality : 0.040 0.120 957 Planarity : 0.005 0.045 1044 Dihedral : 21.502 171.127 1953 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.60 % Allowed : 16.59 % Favored : 80.81 % 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: 0.89 (0.31), residues: 714 helix: 1.24 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.024 0.002 TYR C 81 PHE 0.023 0.002 PHE A 144 TRP 0.013 0.002 TRP B 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7026) covalent geometry : angle 0.60816 / 0.29 ( 9465) hydrogen bonds : bond 0.04435 / 2.96 ( 372) hydrogen bonds : angle 4.50703 / 3.23 ( 1116) Misc. bond : bond 0.00028 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6580 (pt0) cc_final: 0.6119 (mp0) REVERT: A 229 ASP cc_start: 0.8133 (m-30) cc_final: 0.7785 (m-30) REVERT: B 51 MET cc_start: 0.5709 (mtt) cc_final: 0.4654 (ttm) REVERT: B 174 LYS cc_start: 0.8446 (tttm) cc_final: 0.7590 (mttp) REVERT: B 218 GLN cc_start: 0.4788 (tt0) cc_final: 0.4473 (tp-100) REVERT: C 240 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6515 (mpp) REVERT: C 249 GLU cc_start: 0.7286 (tp30) cc_final: 0.6998 (tt0) outliers start: 16 outliers final: 11 residues processed: 142 average time/residue: 0.0655 time to fit residues: 12.9087 Evaluate side-chains 133 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4176 r_free = 0.4176 target = 0.188073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.162807 restraints weight = 6956.914| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.42 r_work: 0.3767 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.165 Angle : 0.624 7.512 9465 Z= 0.303 Chirality : 0.041 0.127 957 Planarity : 0.005 0.047 1044 Dihedral : 20.329 179.774 1953 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.60 % Allowed : 18.70 % Favored : 78.70 % 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: 1.01 (0.31), residues: 714 helix: 1.25 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.78 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.023 0.002 TYR A 45 PHE 0.025 0.002 PHE A 144 TRP 0.016 0.002 TRP B 42 HIS 0.002 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7026) covalent geometry : angle 0.62412 / 0.30 ( 9465) hydrogen bonds : bond 0.04428 / 2.91 ( 372) hydrogen bonds : angle 4.55927 / 3.26 ( 1116) Misc. bond : bond 0.00041 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 MET cc_start: 0.5922 (mtt) cc_final: 0.5698 (mtm) REVERT: B 174 LYS cc_start: 0.8530 (tttm) cc_final: 0.7520 (mttp) REVERT: B 218 GLN cc_start: 0.5109 (tt0) cc_final: 0.4717 (tp-100) REVERT: C 240 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6562 (mpp) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.0635 time to fit residues: 12.4023 Evaluate side-chains 127 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS ** C 125 HIS ** 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 = 0.4176 r_free = 0.4176 target = 0.188386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162899 restraints weight = 6893.908| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.42 r_work: 0.3768 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.151 Angle : 0.610 8.074 9465 Z= 0.298 Chirality : 0.041 0.119 957 Planarity : 0.005 0.043 1044 Dihedral : 18.980 168.384 1953 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 20.33 % Favored : 77.40 % 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: 1.12 (0.31), residues: 714 helix: 1.30 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.023 0.002 TYR A 45 PHE 0.026 0.002 PHE A 144 TRP 0.017 0.002 TRP B 187 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 7026) covalent geometry : angle 0.60976 / 0.30 ( 9465) hydrogen bonds : bond 0.04318 / 2.83 ( 372) hydrogen bonds : angle 4.51123 / 3.22 ( 1116) Misc. bond : bond 0.00030 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.7010 (t80) cc_final: 0.6810 (t80) REVERT: B 51 MET cc_start: 0.5959 (mtt) cc_final: 0.5758 (mtm) REVERT: B 174 LYS cc_start: 0.8515 (tttm) cc_final: 0.7524 (mttp) REVERT: B 209 SER cc_start: 0.8361 (p) cc_final: 0.8071 (m) REVERT: C 240 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6532 (mpp) REVERT: C 249 GLU cc_start: 0.7542 (tp30) cc_final: 0.6747 (tt0) outliers start: 14 outliers final: 13 residues processed: 144 average time/residue: 0.0613 time to fit residues: 12.1227 Evaluate side-chains 128 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 HIS ** C 125 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.188076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.162622 restraints weight = 6837.590| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.41 r_work: 0.3760 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7032 Z= 0.160 Angle : 0.634 10.014 9465 Z= 0.309 Chirality : 0.041 0.146 957 Planarity : 0.005 0.041 1044 Dihedral : 18.577 158.407 1953 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 20.81 % Favored : 76.75 % 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: 1.13 (0.31), residues: 714 helix: 1.30 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.57 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 186 TYR 0.023 0.002 TYR A 45 PHE 0.027 0.002 PHE A 144 TRP 0.016 0.002 TRP B 187 HIS 0.010 0.001 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 7026) covalent geometry : angle 0.63387 / 0.31 ( 9465) hydrogen bonds : bond 0.04383 / 2.86 ( 372) hydrogen bonds : angle 4.56085 / 3.25 ( 1116) Misc. bond : bond 0.00027 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 PHE cc_start: 0.7101 (t80) cc_final: 0.6824 (t80) REVERT: B 155 TYR cc_start: 0.6324 (t80) cc_final: 0.6114 (t80) REVERT: B 174 LYS cc_start: 0.8528 (tttm) cc_final: 0.7515 (mttp) REVERT: B 209 SER cc_start: 0.8330 (p) cc_final: 0.8051 (m) REVERT: C 240 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6794 (mpp) REVERT: C 249 GLU cc_start: 0.7359 (tp30) cc_final: 0.6616 (tt0) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.0558 time to fit residues: 11.1767 Evaluate side-chains 132 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 67 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4179 r_free = 0.4179 target = 0.188281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162599 restraints weight = 6814.111| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.43 r_work: 0.3780 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7032 Z= 0.137 Angle : 0.594 8.625 9465 Z= 0.293 Chirality : 0.040 0.157 957 Planarity : 0.005 0.040 1044 Dihedral : 17.651 151.969 1953 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.28 % Allowed : 21.14 % Favored : 76.59 % 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: 1.25 (0.31), residues: 714 helix: 1.39 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.54 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 186 TYR 0.022 0.002 TYR A 45 PHE 0.027 0.002 PHE A 144 TRP 0.019 0.002 TRP B 199 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7026) covalent geometry : angle 0.59433 / 0.29 ( 9465) hydrogen bonds : bond 0.04245 / 2.77 ( 372) hydrogen bonds : angle 4.46321 / 3.18 ( 1116) Misc. bond : bond 0.00017 / 0.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7377 (tpt90) cc_final: 0.7153 (tpt170) REVERT: B 174 LYS cc_start: 0.8547 (tttm) cc_final: 0.7586 (mttp) REVERT: B 209 SER cc_start: 0.8303 (p) cc_final: 0.8014 (m) REVERT: C 240 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6351 (mpp) REVERT: C 249 GLU cc_start: 0.7381 (tp30) cc_final: 0.6640 (tt0) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.0663 time to fit residues: 13.0935 Evaluate side-chains 134 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161735 restraints weight = 6766.199| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.44 r_work: 0.3762 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7032 Z= 0.152 Angle : 0.618 9.190 9465 Z= 0.308 Chirality : 0.041 0.202 957 Planarity : 0.005 0.041 1044 Dihedral : 17.064 161.757 1953 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.95 % Allowed : 21.79 % Favored : 76.26 % 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: 1.25 (0.31), residues: 714 helix: 1.38 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 186 TYR 0.020 0.002 TYR B 177 PHE 0.029 0.002 PHE A 144 TRP 0.017 0.002 TRP B 199 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 7026) covalent geometry : angle 0.61776 / 0.31 ( 9465) hydrogen bonds : bond 0.04380 / 2.86 ( 372) hydrogen bonds : angle 4.51563 / 3.22 ( 1116) Misc. bond : bond 0.00023 / 0.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.7660 (mtt) cc_final: 0.7397 (mtt) REVERT: B 46 ARG cc_start: 0.7382 (tpt90) cc_final: 0.7147 (tpt170) REVERT: B 106 TYR cc_start: 0.7217 (m-80) cc_final: 0.6896 (m-80) REVERT: B 174 LYS cc_start: 0.8436 (tttm) cc_final: 0.7491 (mttp) REVERT: B 209 SER cc_start: 0.8326 (p) cc_final: 0.8064 (m) REVERT: C 240 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6568 (mpp) REVERT: C 249 GLU cc_start: 0.7329 (tp30) cc_final: 0.6634 (tt0) outliers start: 12 outliers final: 11 residues processed: 140 average time/residue: 0.0626 time to fit residues: 11.8749 Evaluate side-chains 139 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.188013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162077 restraints weight = 6770.294| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.44 r_work: 0.3752 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.7187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7032 Z= 0.143 Angle : 0.617 9.045 9465 Z= 0.309 Chirality : 0.041 0.137 957 Planarity : 0.005 0.043 1044 Dihedral : 16.610 179.346 1953 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.11 % Allowed : 21.46 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.31), residues: 714 helix: 1.34 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.44 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 186 TYR 0.052 0.002 TYR A 81 PHE 0.030 0.002 PHE A 144 TRP 0.017 0.002 TRP B 199 HIS 0.006 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 7026) covalent geometry : angle 0.61719 / 0.31 ( 9465) hydrogen bonds : bond 0.04385 / 2.87 ( 372) hydrogen bonds : angle 4.51454 / 3.23 ( 1116) Misc. bond : bond 0.00022 / 0.01 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7528 (mmtt) REVERT: A 180 TYR cc_start: 0.5850 (m-10) cc_final: 0.5585 (m-10) REVERT: A 189 PHE cc_start: 0.7274 (t80) cc_final: 0.6858 (t80) REVERT: B 106 TYR cc_start: 0.7148 (m-80) cc_final: 0.6831 (m-80) REVERT: B 174 LYS cc_start: 0.8391 (tttm) cc_final: 0.7480 (mttp) REVERT: B 209 SER cc_start: 0.8265 (p) cc_final: 0.8004 (m) REVERT: C 116 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6916 (p0) REVERT: C 240 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6413 (mpp) REVERT: C 249 GLU cc_start: 0.7296 (tp30) cc_final: 0.6624 (tt0) outliers start: 13 outliers final: 11 residues processed: 142 average time/residue: 0.0669 time to fit residues: 13.0845 Evaluate side-chains 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 125 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.186886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.161409 restraints weight = 6709.163| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.41 r_work: 0.3747 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7032 Z= 0.153 Angle : 0.631 9.335 9465 Z= 0.314 Chirality : 0.041 0.124 957 Planarity : 0.005 0.046 1044 Dihedral : 16.365 157.060 1953 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.11 % Allowed : 21.79 % Favored : 76.10 % 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: 1.23 (0.31), residues: 714 helix: 1.34 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.47 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 186 TYR 0.059 0.002 TYR A 81 PHE 0.029 0.002 PHE A 144 TRP 0.017 0.002 TRP B 199 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 7026) covalent geometry : angle 0.63091 / 0.31 ( 9465) hydrogen bonds : bond 0.04451 / 2.91 ( 372) hydrogen bonds : angle 4.51627 / 3.23 ( 1116) Misc. bond : bond 0.00018 / 0.01 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1442.35 seconds wall clock time: 25 minutes 29.92 seconds (1529.92 seconds total)