Starting phenix.real_space_refine on Tue Aug 4 21:10:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469.map" model { file = "/net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cde_45469/08_2026/9cde_45469_neut.cif" } resolution = 3.44 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= 0.008 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 1089 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: 6822 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: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 320 Unusual residues: {'CLR': 3, 'PEE': 4, 'RET': 1} Classifications: {'undetermined': 8, 'water': 12} Link IDs: {None: 19} 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: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Restraints were copied for chains: B, C Time building chain proxies: 1.63, per 1000 atoms: 0.24 Number of scatterers: 6822 At special positions: 0 Unit cell: (80.34, 76.22, 75.19, 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 1089 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: 0.64 Conformation dependent library (CDL) restraints added in 306.9 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: 33 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 50 removed outlier: 3.681A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.527A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.568A pdb=" N ILE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 142 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: 3.827A pdb=" N HIS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 4.204A pdb=" N TRP A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.681A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.527A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix removed outlier: 3.568A pdb=" N ILE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 142 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: 3.826A pdb=" N HIS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 removed outlier: 4.203A pdb=" N TRP B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 3.681A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.527A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 122 removed outlier: 3.919A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix removed outlier: 3.568A pdb=" N ILE C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 142 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: 3.827A pdb=" N HIS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 removed outlier: 4.203A pdb=" N TRP C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.784A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.516A pdb=" N ILE C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 252 378 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.79 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: 1399 1.33 - 1.45: 1666 1.45 - 1.57: 3820 1.57 - 1.69: 51 1.69 - 1.81: 90 Bond restraints: 7026 Sorted by residual: bond pdb=" O4P PEE C 305 " pdb=" P PEE C 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4P PEE A 305 " pdb=" P PEE A 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O4P PEE B 305 " pdb=" P PEE B 305 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.80e+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 3.79e+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 ... (remaining 7021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 9110 2.78 - 5.56: 250 5.56 - 8.34: 90 8.34 - 11.11: 3 11.11 - 13.89: 12 Bond angle restraints: 9465 Sorted by residual: angle pdb=" O1P PEE A 308 " pdb=" P PEE A 308 " pdb=" O2P PEE A 308 " ideal model delta sigma weight residual 119.43 133.32 -13.89 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE B 308 " pdb=" P PEE B 308 " pdb=" O2P PEE B 308 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE C 308 " pdb=" P PEE C 308 " pdb=" O2P PEE C 308 " ideal model delta sigma weight residual 119.43 133.31 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" O1P PEE C 307 " pdb=" P PEE C 307 " pdb=" O2P PEE C 307 " ideal model delta sigma weight residual 119.43 133.27 -13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE A 306 " pdb=" P PEE A 306 " pdb=" O2P PEE A 306 " ideal model delta sigma weight residual 119.43 133.27 -13.84 3.00e+00 1.11e-01 2.13e+01 ... (remaining 9460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 4236 34.41 - 68.82: 234 68.82 - 103.23: 27 103.23 - 137.64: 12 137.64 - 172.05: 36 Dihedral angle restraints: 4545 sinusoidal: 2451 harmonic: 2094 Sorted by residual: 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 -56.97 115.08 -172.05 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 -56.97 115.04 -172.01 1 3.00e+01 1.11e-03 2.12e+01 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 -56.97 115.03 -172.00 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 4542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 856 0.087 - 0.173: 53 0.173 - 0.260: 3 0.260 - 0.347: 30 0.347 - 0.433: 15 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 4.69e+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 4.68e+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 4.67e+00 ... (remaining 954 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET C 301 " -0.027 2.00e-02 2.50e+03 7.21e-02 6.51e+01 pdb=" C13 RET C 301 " 0.049 2.00e-02 2.50e+03 pdb=" C14 RET C 301 " -0.128 2.00e-02 2.50e+03 pdb=" C15 RET C 301 " 0.074 2.00e-02 2.50e+03 pdb=" C20 RET C 301 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET A 301 " 0.027 2.00e-02 2.50e+03 7.19e-02 6.47e+01 pdb=" C13 RET A 301 " -0.049 2.00e-02 2.50e+03 pdb=" C14 RET A 301 " 0.128 2.00e-02 2.50e+03 pdb=" C15 RET A 301 " -0.074 2.00e-02 2.50e+03 pdb=" C20 RET A 301 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET B 301 " 0.027 2.00e-02 2.50e+03 7.18e-02 6.45e+01 pdb=" C13 RET B 301 " -0.049 2.00e-02 2.50e+03 pdb=" C14 RET B 301 " 0.127 2.00e-02 2.50e+03 pdb=" C15 RET B 301 " -0.074 2.00e-02 2.50e+03 pdb=" C20 RET B 301 " -0.032 2.00e-02 2.50e+03 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 126 2.60 - 3.18: 5844 3.18 - 3.75: 10839 3.75 - 4.33: 16239 4.33 - 4.90: 25811 Nonbonded interactions: 58859 Sorted by model distance: nonbonded pdb=" N ILE A 127 " pdb=" OE2 GLU C 65 " model vdw 2.031 3.120 nonbonded pdb=" OE2 GLU B 65 " pdb=" N ILE C 127 " model vdw 2.034 3.120 nonbonded pdb=" OE2 GLU A 65 " pdb=" N ILE B 127 " model vdw 2.036 3.120 nonbonded pdb=" O SER C 168 " pdb=" ND1 HIS C 172 " model vdw 2.254 3.120 nonbonded pdb=" O SER A 168 " pdb=" ND1 HIS A 172 " model vdw 2.254 3.120 ... (remaining 58854 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.400 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 0.343 7032 Z= 0.864 Angle : 1.152 13.892 9465 Z= 0.425 Chirality : 0.084 0.433 957 Planarity : 0.006 0.072 1044 Dihedral : 25.586 172.045 3213 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.46 % Allowed : 4.88 % Favored : 93.66 % 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 (0.33), residues: 714 helix: 1.71 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.014 0.002 TYR A 53 PHE 0.020 0.001 PHE B 196 TRP 0.006 0.001 TRP C 42 HIS 0.001 0.000 HIS C 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00942 / 0.46 ( 7026) covalent geometry : angle 1.15223 / 0.43 ( 9465) hydrogen bonds : bond 0.21549 / 14.57 ( 378) hydrogen bonds : angle 6.45900 / 4.55 ( 1134) Misc. bond : bond 0.24981 / 12.09 ( 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 299 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 290 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.8437 (p) cc_final: 0.8230 (p) REVERT: A 155 TYR cc_start: 0.8144 (t80) cc_final: 0.7362 (t80) REVERT: A 180 TYR cc_start: 0.6083 (m-10) cc_final: 0.5854 (m-10) REVERT: A 195 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6496 (t80) REVERT: B 65 GLU cc_start: 0.8203 (tp30) cc_final: 0.7667 (mp0) REVERT: B 151 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7588 (ttm170) REVERT: B 155 TYR cc_start: 0.8185 (t80) cc_final: 0.7904 (t80) REVERT: B 185 GLN cc_start: 0.8513 (mt0) cc_final: 0.8300 (mt0) REVERT: B 195 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6229 (t80) REVERT: B 247 LEU cc_start: 0.8702 (mt) cc_final: 0.8500 (mm) REVERT: C 65 GLU cc_start: 0.8175 (tp30) cc_final: 0.7927 (mp0) REVERT: C 101 TYR cc_start: 0.7606 (m-10) cc_final: 0.7136 (m-10) REVERT: C 151 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7738 (ttm170) REVERT: C 155 TYR cc_start: 0.8039 (t80) cc_final: 0.7620 (t80) REVERT: C 177 TYR cc_start: 0.8577 (t80) cc_final: 0.7399 (t80) REVERT: C 180 TYR cc_start: 0.6126 (m-10) cc_final: 0.5746 (m-10) REVERT: C 185 GLN cc_start: 0.8433 (mt0) cc_final: 0.7727 (mt0) REVERT: C 195 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6290 (t80) outliers start: 9 outliers final: 0 residues processed: 294 average time/residue: 0.0741 time to fit residues: 29.3853 Evaluate side-chains 205 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain C residue 195 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 225 HIS B 99 ASN B 225 HIS C 99 ASN C 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154272 restraints weight = 9273.555| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.11 r_work: 0.3694 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7032 Z= 0.157 Angle : 0.666 7.372 9465 Z= 0.324 Chirality : 0.041 0.122 957 Planarity : 0.005 0.033 1044 Dihedral : 26.133 176.417 1959 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.63 % Allowed : 18.05 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.32), residues: 714 helix: 1.49 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 151 TYR 0.016 0.002 TYR C 53 PHE 0.029 0.002 PHE C 86 TRP 0.010 0.002 TRP A 161 HIS 0.014 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7026) covalent geometry : angle 0.66556 / 0.32 ( 9465) hydrogen bonds : bond 0.04398 / 2.98 ( 378) hydrogen bonds : angle 4.85711 / 3.47 ( 1134) Misc. bond : bond 0.00052 / 0.03 ( 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 255 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 SER cc_start: 0.7665 (p) cc_final: 0.7417 (m) REVERT: A 155 TYR cc_start: 0.8075 (t80) cc_final: 0.7337 (t80) REVERT: A 168 SER cc_start: 0.7574 (t) cc_final: 0.7362 (p) REVERT: B 43 MET cc_start: 0.7417 (ptp) cc_final: 0.7060 (mtm) REVERT: B 155 TYR cc_start: 0.8237 (t80) cc_final: 0.8004 (t80) REVERT: B 165 PHE cc_start: 0.7995 (t80) cc_final: 0.7790 (t80) REVERT: B 177 TYR cc_start: 0.8720 (t80) cc_final: 0.8442 (t80) REVERT: B 195 PHE cc_start: 0.6962 (t80) cc_final: 0.6674 (t80) REVERT: C 43 MET cc_start: 0.7579 (ptp) cc_final: 0.7365 (mtm) REVERT: C 86 PHE cc_start: 0.8633 (m-80) cc_final: 0.8389 (m-80) REVERT: C 101 TYR cc_start: 0.7607 (m-10) cc_final: 0.7406 (m-10) REVERT: C 155 TYR cc_start: 0.8061 (t80) cc_final: 0.7627 (t80) REVERT: C 195 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5979 (t80) REVERT: C 229 ASP cc_start: 0.6413 (m-30) cc_final: 0.6156 (m-30) outliers start: 10 outliers final: 5 residues processed: 247 average time/residue: 0.0592 time to fit residues: 20.8612 Evaluate side-chains 196 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 195 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN B 219 GLN B 225 HIS C 185 GLN C 219 GLN C 225 HIS C 250 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.185381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.158058 restraints weight = 8976.208| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.13 r_work: 0.3712 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7032 Z= 0.186 Angle : 0.701 12.757 9465 Z= 0.336 Chirality : 0.043 0.181 957 Planarity : 0.005 0.033 1044 Dihedral : 24.519 179.451 1955 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.95 % Allowed : 22.60 % Favored : 75.45 % 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: 0.71 (0.32), residues: 714 helix: 1.25 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.56 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 151 TYR 0.017 0.002 TYR B 106 PHE 0.024 0.002 PHE A 243 TRP 0.009 0.001 TRP C 199 HIS 0.009 0.002 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 ( 7026) covalent geometry : angle 0.70066 / 0.34 ( 9465) hydrogen bonds : bond 0.04384 / 2.94 ( 378) hydrogen bonds : angle 4.75800 / 3.40 ( 1134) Misc. bond : bond 0.00062 / 0.03 ( 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 227 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 SER cc_start: 0.7806 (t) cc_final: 0.7506 (p) REVERT: A 195 PHE cc_start: 0.6800 (t80) cc_final: 0.6562 (t80) REVERT: B 155 TYR cc_start: 0.8230 (t80) cc_final: 0.8006 (t80) REVERT: B 177 TYR cc_start: 0.8522 (t80) cc_final: 0.7608 (t80) REVERT: C 43 MET cc_start: 0.7654 (ptp) cc_final: 0.7216 (mtm) REVERT: C 101 TYR cc_start: 0.7725 (m-10) cc_final: 0.7492 (m-10) REVERT: C 155 TYR cc_start: 0.8114 (t80) cc_final: 0.7642 (t80) REVERT: C 177 TYR cc_start: 0.8549 (t80) cc_final: 0.7750 (t80) outliers start: 12 outliers final: 5 residues processed: 222 average time/residue: 0.0587 time to fit residues: 18.3638 Evaluate side-chains 194 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS B 218 GLN B 219 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.190540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164645 restraints weight = 9142.402| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.22 r_work: 0.3738 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7032 Z= 0.143 Angle : 0.656 11.124 9465 Z= 0.320 Chirality : 0.042 0.187 957 Planarity : 0.005 0.031 1044 Dihedral : 23.080 168.924 1953 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 23.58 % Favored : 73.98 % 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: 0.76 (0.32), residues: 714 helix: 1.24 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 46 TYR 0.022 0.002 TYR C 45 PHE 0.037 0.002 PHE C 86 TRP 0.023 0.001 TRP B 42 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 7026) covalent geometry : angle 0.65617 / 0.32 ( 9465) hydrogen bonds : bond 0.03891 / 2.58 ( 378) hydrogen bonds : angle 4.67783 / 3.34 ( 1134) Misc. bond : bond 0.00077 / 0.05 ( 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 228 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7055 (m-30) cc_final: 0.6794 (m-30) REVERT: B 67 ASN cc_start: 0.8329 (m-40) cc_final: 0.8013 (m-40) REVERT: B 184 CYS cc_start: 0.8316 (m) cc_final: 0.7872 (m) REVERT: C 46 ARG cc_start: 0.6966 (mmm160) cc_final: 0.6759 (mmm160) REVERT: C 86 PHE cc_start: 0.8571 (m-80) cc_final: 0.8366 (m-80) REVERT: C 101 TYR cc_start: 0.7653 (m-10) cc_final: 0.7396 (m-10) REVERT: C 177 TYR cc_start: 0.8344 (t80) cc_final: 0.7535 (t80) REVERT: C 185 GLN cc_start: 0.8598 (mt0) cc_final: 0.8058 (mm110) REVERT: C 229 ASP cc_start: 0.7005 (m-30) cc_final: 0.6768 (m-30) outliers start: 15 outliers final: 7 residues processed: 222 average time/residue: 0.0715 time to fit residues: 22.3173 Evaluate side-chains 197 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 218 GLN B 219 GLN C 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151283 restraints weight = 9198.391| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.43 r_work: 0.3601 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4757 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= 0.138 Angle : 0.687 17.880 9465 Z= 0.329 Chirality : 0.042 0.196 957 Planarity : 0.005 0.035 1044 Dihedral : 21.781 155.401 1953 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.41 % Allowed : 24.88 % Favored : 71.71 % 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: 0.77 (0.32), residues: 714 helix: 1.22 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.22 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 176 TYR 0.023 0.002 TYR C 45 PHE 0.028 0.002 PHE C 86 TRP 0.009 0.001 TRP B 42 HIS 0.006 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 7026) covalent geometry : angle 0.68657 / 0.33 ( 9465) hydrogen bonds : bond 0.03889 / 2.58 ( 378) hydrogen bonds : angle 4.61305 / 3.28 ( 1134) Misc. bond : bond 0.00034 / 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 236 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7322 (mp0) cc_final: 0.7028 (mp0) REVERT: A 98 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7512 (tt) REVERT: B 45 TYR cc_start: 0.6397 (t80) cc_final: 0.6153 (t80) REVERT: B 177 TYR cc_start: 0.8483 (t80) cc_final: 0.8027 (t80) REVERT: C 101 TYR cc_start: 0.7772 (m-10) cc_final: 0.7478 (m-10) REVERT: C 177 TYR cc_start: 0.8435 (t80) cc_final: 0.7927 (t80) REVERT: C 229 ASP cc_start: 0.6921 (m-30) cc_final: 0.6576 (m-30) outliers start: 21 outliers final: 6 residues processed: 229 average time/residue: 0.0696 time to fit residues: 22.3872 Evaluate side-chains 198 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN C 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.178663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151138 restraints weight = 9339.119| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.37 r_work: 0.3610 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7032 Z= 0.146 Angle : 0.718 17.100 9465 Z= 0.342 Chirality : 0.043 0.206 957 Planarity : 0.005 0.032 1044 Dihedral : 20.585 159.863 1953 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.60 % Allowed : 27.32 % Favored : 70.08 % 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 (0.31), residues: 714 helix: 1.12 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.15 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 46 TYR 0.022 0.002 TYR C 45 PHE 0.041 0.002 PHE C 86 TRP 0.008 0.001 TRP A 199 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7026) covalent geometry : angle 0.71844 / 0.34 ( 9465) hydrogen bonds : bond 0.03944 / 2.61 ( 378) hydrogen bonds : angle 4.65369 / 3.29 ( 1134) Misc. bond : bond 0.00039 / 0.03 ( 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 221 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 229 ASP cc_start: 0.6948 (m-30) cc_final: 0.6591 (m-30) REVERT: B 174 LYS cc_start: 0.7298 (mptt) cc_final: 0.7062 (mmtt) REVERT: B 177 TYR cc_start: 0.8540 (t80) cc_final: 0.7983 (t80) REVERT: C 43 MET cc_start: 0.7437 (ptp) cc_final: 0.6973 (mtm) REVERT: C 46 ARG cc_start: 0.6034 (mmm160) cc_final: 0.5642 (mmm160) REVERT: C 101 TYR cc_start: 0.7744 (m-10) cc_final: 0.7448 (m-10) REVERT: C 177 TYR cc_start: 0.8424 (t80) cc_final: 0.7908 (t80) outliers start: 16 outliers final: 9 residues processed: 217 average time/residue: 0.0726 time to fit residues: 21.9524 Evaluate side-chains 203 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 145 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 0.0030 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 0.0060 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 219 GLN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.180271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.152886 restraints weight = 9130.161| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.35 r_work: 0.3631 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7032 Z= 0.137 Angle : 0.700 17.621 9465 Z= 0.338 Chirality : 0.043 0.209 957 Planarity : 0.005 0.035 1044 Dihedral : 19.706 163.963 1953 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.09 % Allowed : 25.85 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 714 helix: 1.09 (0.23), residues: 510 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.023 0.002 TYR C 45 PHE 0.050 0.002 PHE C 86 TRP 0.034 0.001 TRP A 199 HIS 0.005 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7026) covalent geometry : angle 0.70035 / 0.34 ( 9465) hydrogen bonds : bond 0.03790 / 2.51 ( 378) hydrogen bonds : angle 4.63834 / 3.28 ( 1134) Misc. bond : bond 0.00023 / 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 225 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 LYS cc_start: 0.7254 (mptt) cc_final: 0.7023 (mmtt) REVERT: B 177 TYR cc_start: 0.8432 (t80) cc_final: 0.7876 (t80) REVERT: B 244 ARG cc_start: 0.7655 (ttm170) cc_final: 0.7336 (ttm170) REVERT: C 43 MET cc_start: 0.7384 (ptp) cc_final: 0.6875 (mtm) REVERT: C 46 ARG cc_start: 0.6029 (mmm160) cc_final: 0.5692 (mmm160) REVERT: C 101 TYR cc_start: 0.7728 (m-10) cc_final: 0.7444 (m-10) REVERT: C 176 ARG cc_start: 0.7679 (mtp-110) cc_final: 0.7310 (ttm110) REVERT: C 177 TYR cc_start: 0.8405 (t80) cc_final: 0.8075 (t80) outliers start: 19 outliers final: 11 residues processed: 219 average time/residue: 0.0706 time to fit residues: 21.3750 Evaluate side-chains 201 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 225 HIS ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN C 219 GLN C 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153732 restraints weight = 9325.826| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.37 r_work: 0.3631 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7032 Z= 0.150 Angle : 0.730 15.856 9465 Z= 0.356 Chirality : 0.043 0.208 957 Planarity : 0.005 0.040 1044 Dihedral : 19.178 161.634 1953 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.25 % Allowed : 28.29 % Favored : 68.46 % 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: 0.53 (0.31), residues: 714 helix: 1.02 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.37 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.025 0.002 TYR C 45 PHE 0.045 0.002 PHE C 86 TRP 0.057 0.001 TRP A 199 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7026) covalent geometry : angle 0.72974 / 0.36 ( 9465) hydrogen bonds : bond 0.03913 / 2.57 ( 378) hydrogen bonds : angle 4.69711 / 3.33 ( 1134) Misc. bond : bond 0.00067 / 0.04 ( 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 216 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7540 (tt) REVERT: A 229 ASP cc_start: 0.6711 (m-30) cc_final: 0.6421 (m-30) REVERT: B 177 TYR cc_start: 0.8404 (t80) cc_final: 0.7880 (t80) REVERT: B 244 ARG cc_start: 0.7669 (ttm170) cc_final: 0.7297 (ttm170) REVERT: C 43 MET cc_start: 0.7369 (ptp) cc_final: 0.6845 (mtm) REVERT: C 46 ARG cc_start: 0.5976 (mmm160) cc_final: 0.5676 (mmm160) REVERT: C 86 PHE cc_start: 0.8514 (m-80) cc_final: 0.8306 (m-80) REVERT: C 101 TYR cc_start: 0.7725 (m-10) cc_final: 0.7446 (m-10) REVERT: C 177 TYR cc_start: 0.7935 (t80) cc_final: 0.7667 (t80) REVERT: C 185 GLN cc_start: 0.8884 (mt0) cc_final: 0.8547 (tp40) outliers start: 20 outliers final: 14 residues processed: 211 average time/residue: 0.0684 time to fit residues: 20.1805 Evaluate side-chains 197 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 225 HIS ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 250 HIS C 219 GLN C 250 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.182312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154745 restraints weight = 9361.629| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.41 r_work: 0.3634 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7032 Z= 0.140 Angle : 0.718 14.573 9465 Z= 0.352 Chirality : 0.044 0.221 957 Planarity : 0.005 0.032 1044 Dihedral : 18.411 170.061 1953 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 2.44 % Allowed : 28.62 % Favored : 68.94 % 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: 0.48 (0.31), residues: 714 helix: 0.96 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 46 TYR 0.027 0.001 TYR C 45 PHE 0.043 0.002 PHE C 86 TRP 0.049 0.001 TRP A 199 HIS 0.011 0.002 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7026) covalent geometry : angle 0.71792 / 0.35 ( 9465) hydrogen bonds : bond 0.03904 / 2.59 ( 378) hydrogen bonds : angle 4.69283 / 3.32 ( 1134) Misc. bond : bond 0.00048 / 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 213 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8246 (mt) cc_final: 0.7954 (mt) REVERT: A 101 TYR cc_start: 0.7629 (m-10) cc_final: 0.7409 (m-10) REVERT: A 228 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7590 (mt) REVERT: A 229 ASP cc_start: 0.6819 (m-30) cc_final: 0.6517 (m-30) REVERT: B 177 TYR cc_start: 0.8328 (t80) cc_final: 0.7806 (t80) REVERT: B 244 ARG cc_start: 0.7713 (ttm170) cc_final: 0.7391 (ttm170) REVERT: C 42 TRP cc_start: 0.6188 (t60) cc_final: 0.5293 (t60) REVERT: C 43 MET cc_start: 0.7330 (ptp) cc_final: 0.6488 (mtm) REVERT: C 46 ARG cc_start: 0.5892 (mmm160) cc_final: 0.5604 (mmm160) REVERT: C 101 TYR cc_start: 0.7703 (m-10) cc_final: 0.7415 (m-10) REVERT: C 185 GLN cc_start: 0.8924 (mt0) cc_final: 0.8662 (tp40) outliers start: 15 outliers final: 11 residues processed: 210 average time/residue: 0.0690 time to fit residues: 20.1676 Evaluate side-chains 194 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 225 HIS A 250 HIS B 250 HIS C 219 GLN C 250 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.182435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155109 restraints weight = 9307.239| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.35 r_work: 0.3654 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7032 Z= 0.146 Angle : 0.736 14.496 9465 Z= 0.362 Chirality : 0.044 0.218 957 Planarity : 0.005 0.036 1044 Dihedral : 18.066 176.444 1953 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.20 % Favored : 95.66 % Rotamer: Outliers : 3.25 % Allowed : 28.62 % Favored : 68.13 % 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: 0.44 (0.31), residues: 714 helix: 0.93 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 46 TYR 0.026 0.002 TYR C 45 PHE 0.058 0.002 PHE C 86 TRP 0.044 0.002 TRP A 199 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7026) covalent geometry : angle 0.73640 / 0.36 ( 9465) hydrogen bonds : bond 0.03957 / 2.61 ( 378) hydrogen bonds : angle 4.73685 / 3.36 ( 1134) Misc. bond : bond 0.00048 / 0.02 ( 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 205 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7597 (mt) REVERT: A 229 ASP cc_start: 0.6807 (m-30) cc_final: 0.6493 (m-30) REVERT: B 177 TYR cc_start: 0.8252 (t80) cc_final: 0.7755 (t80) REVERT: B 244 ARG cc_start: 0.7759 (ttm170) cc_final: 0.7391 (ttm170) REVERT: C 42 TRP cc_start: 0.6210 (t60) cc_final: 0.5414 (t60) REVERT: C 43 MET cc_start: 0.7271 (ptp) cc_final: 0.6740 (mtm) REVERT: C 46 ARG cc_start: 0.5910 (mmm160) cc_final: 0.5654 (mmm160) REVERT: C 101 TYR cc_start: 0.7693 (m-10) cc_final: 0.7408 (m-10) REVERT: C 177 TYR cc_start: 0.8203 (t80) cc_final: 0.7837 (t80) outliers start: 20 outliers final: 14 residues processed: 202 average time/residue: 0.0748 time to fit residues: 20.9688 Evaluate side-chains 199 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 250 HIS ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.185344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.158062 restraints weight = 9352.972| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.36 r_work: 0.3689 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7032 Z= 0.135 Angle : 0.745 18.851 9465 Z= 0.363 Chirality : 0.044 0.223 957 Planarity : 0.005 0.056 1044 Dihedral : 17.546 178.869 1953 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.78 % Favored : 96.08 % Rotamer: Outliers : 2.28 % Allowed : 29.27 % Favored : 68.46 % 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: 0.44 (0.31), residues: 714 helix: 0.93 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.029 0.001 TYR C 45 PHE 0.053 0.002 PHE C 86 TRP 0.067 0.002 TRP A 42 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7026) covalent geometry : angle 0.74490 / 0.36 ( 9465) hydrogen bonds : bond 0.03868 / 2.56 ( 378) hydrogen bonds : angle 4.70921 / 3.33 ( 1134) Misc. bond : bond 0.00043 / 0.02 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.42 seconds wall clock time: 26 minutes 27.24 seconds (1587.24 seconds total)