Starting phenix.real_space_refine on Tue Mar 11 23:34:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdd_45468/03_2025/9cdd_45468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdd_45468/03_2025/9cdd_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_45468/03_2025/9cdd_45468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdd_45468/03_2025/9cdd_45468.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdd_45468/03_2025/9cdd_45468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdd_45468/03_2025/9cdd_45468_neut.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B Time building chain proxies: 4.42, per 1000 atoms: 0.64 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: 2.02 Conformation dependent library (CDL) restraints added in 888.6 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: 0.56 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: 1.78 Time building geometry restraints manager: 2.35 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.009 0.125 7026 Z= 0.573 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 : 22.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP B 190 HIS 0.002 0.001 HIS B 125 PHE 0.019 0.002 PHE B 195 TYR 0.012 0.002 TYR B 103 ARG 0.002 0.001 ARG C 151 *********************** 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 : 0.655 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.3217 (mtt) cc_final: 0.2997 (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: 0.6955 (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: 0.7088 (mt) REVERT: C 35 PHE cc_start: 0.7394 (t80) cc_final: 0.6476 (t80) REVERT: C 134 PHE cc_start: 0.7570 (t80) cc_final: 0.7318 (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: 0.7487 (m) outliers start: 12 outliers final: 6 residues processed: 184 average time/residue: 0.1799 time to fit residues: 44.5372 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 : 0.656 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.1980 chunk 54 optimal weight: 0.0060 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 overall best weight: 0.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 225 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.197152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.173732 restraints weight = 6824.811| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.36 r_work: 0.3895 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.401 7026 Z= 0.825 Angle : 1.612 32.288 9465 Z= 0.852 Chirality : 0.079 0.907 957 Planarity : 0.016 0.143 1044 Dihedral : 29.459 173.774 1964 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.23 % Allowed : 13.82 % Favored : 81.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.28), residues: 714 helix: -1.16 (0.21), residues: 498 sheet: None (None), residues: 0 loop : -2.87 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.009 TRP B 138 HIS 0.108 0.013 HIS B 225 PHE 0.225 0.009 PHE C 189 TYR 0.264 0.011 TYR B 106 ARG 0.033 0.003 ARG B 128 *********************** 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 164 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7399 (mm) cc_final: 0.6914 (mm) REVERT: A 51 MET cc_start: 0.3584 (mtt) cc_final: 0.3223 (mtm) REVERT: B 51 MET cc_start: 0.4179 (mtt) cc_final: 0.3765 (ttm) REVERT: B 106 TYR cc_start: 0.6099 (m-10) cc_final: 0.5897 (m-80) REVERT: B 235 ILE cc_start: 0.7499 (mt) cc_final: 0.7209 (mt) REVERT: C 35 PHE cc_start: 0.7421 (t80) cc_final: 0.7054 (t80) REVERT: C 51 MET cc_start: 0.4338 (mtp) cc_final: 0.3817 (tpt) REVERT: C 171 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6521 (ttp80) REVERT: C 177 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.4819 (t80) outliers start: 26 outliers final: 18 residues processed: 155 average time/residue: 0.1722 time to fit residues: 36.2156 Evaluate side-chains 136 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 189 PHE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN B 225 HIS C 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.192786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.168021 restraints weight = 6874.904| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.43 r_work: 0.3833 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7026 Z= 0.268 Angle : 0.653 6.850 9465 Z= 0.320 Chirality : 0.041 0.141 957 Planarity : 0.005 0.037 1044 Dihedral : 25.814 176.975 1964 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.93 % Allowed : 15.61 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 714 helix: 0.30 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.61 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 42 HIS 0.005 0.002 HIS B 125 PHE 0.025 0.002 PHE B 195 TYR 0.030 0.002 TYR A 81 ARG 0.006 0.001 ARG C 176 *********************** 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 163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.6697 (m-80) cc_final: 0.6283 (m-80) REVERT: A 106 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5269 (m-10) REVERT: A 187 TRP cc_start: 0.6955 (m100) cc_final: 0.6547 (m100) REVERT: A 229 ASP cc_start: 0.7504 (m-30) cc_final: 0.6957 (m-30) REVERT: A 231 THR cc_start: 0.6859 (p) cc_final: 0.6651 (p) REVERT: B 47 LEU cc_start: 0.8074 (tp) cc_final: 0.7803 (tp) REVERT: B 51 MET cc_start: 0.4547 (mtt) cc_final: 0.3932 (ttm) REVERT: B 171 ARG cc_start: 0.6534 (mtm110) cc_final: 0.5973 (mtm110) REVERT: B 218 GLN cc_start: 0.5213 (tt0) cc_final: 0.4025 (tp-100) REVERT: B 240 MET cc_start: 0.7211 (tpp) cc_final: 0.6863 (tpp) REVERT: C 81 TYR cc_start: 0.7735 (m-80) cc_final: 0.7442 (m-80) REVERT: C 229 ASP cc_start: 0.8070 (m-30) cc_final: 0.7590 (m-30) REVERT: C 240 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6587 (mpp) outliers start: 18 outliers final: 9 residues processed: 157 average time/residue: 0.1724 time to fit residues: 36.8059 Evaluate side-chains 131 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 106 TYR 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 230 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 240 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS ** 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 = 0.4202 r_free = 0.4202 target = 0.189191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164328 restraints weight = 6966.659| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.42 r_work: 0.3796 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7026 Z= 0.259 Angle : 0.649 8.028 9465 Z= 0.315 Chirality : 0.042 0.167 957 Planarity : 0.005 0.042 1044 Dihedral : 22.830 172.910 1954 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.93 % Allowed : 16.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.31), residues: 714 helix: 0.81 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -1.27 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 42 HIS 0.003 0.001 HIS A 225 PHE 0.025 0.002 PHE B 195 TYR 0.041 0.002 TYR B 81 ARG 0.006 0.001 ARG A 186 *********************** 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 155 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.6394 (m-80) cc_final: 0.6156 (m-80) REVERT: A 175 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6943 (pt0) REVERT: A 187 TRP cc_start: 0.6836 (m100) cc_final: 0.6513 (m100) REVERT: A 189 PHE cc_start: 0.7026 (t80) cc_final: 0.6717 (t80) REVERT: B 105 ASP cc_start: 0.7835 (p0) cc_final: 0.7630 (p0) REVERT: B 174 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7438 (mttp) REVERT: B 186 ARG cc_start: 0.6843 (ttp-110) cc_final: 0.6574 (ptm160) REVERT: B 218 GLN cc_start: 0.5501 (tt0) cc_final: 0.4441 (tp-100) REVERT: C 51 MET cc_start: 0.4112 (mtp) cc_final: 0.3739 (ttp) REVERT: C 240 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6586 (mpp) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 0.1872 time to fit residues: 38.0883 Evaluate side-chains 141 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 234 SER 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 44 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.192610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167470 restraints weight = 6739.169| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.44 r_work: 0.3828 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7026 Z= 0.188 Angle : 0.583 10.253 9465 Z= 0.282 Chirality : 0.039 0.126 957 Planarity : 0.005 0.051 1044 Dihedral : 21.189 175.970 1953 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 17.89 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.31), residues: 714 helix: 1.17 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.14 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 42 HIS 0.003 0.001 HIS A 225 PHE 0.023 0.001 PHE A 144 TYR 0.022 0.002 TYR B 45 ARG 0.007 0.000 ARG A 186 *********************** 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 163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7134 (ttp-110) cc_final: 0.6925 (ttm110) REVERT: A 189 PHE cc_start: 0.7073 (t80) cc_final: 0.6736 (t80) REVERT: A 229 ASP cc_start: 0.7948 (m-30) cc_final: 0.7697 (m-30) REVERT: B 105 ASP cc_start: 0.7699 (p0) cc_final: 0.7477 (p0) REVERT: B 150 TYR cc_start: 0.6877 (m-80) cc_final: 0.6523 (m-80) REVERT: B 174 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7436 (mttp) REVERT: B 186 ARG cc_start: 0.6814 (ttp-110) cc_final: 0.6564 (ptm160) REVERT: B 240 MET cc_start: 0.6843 (mmp) cc_final: 0.6571 (tpt) REVERT: C 51 MET cc_start: 0.4382 (mtp) cc_final: 0.3992 (ttm) REVERT: C 81 TYR cc_start: 0.7889 (m-80) cc_final: 0.7539 (m-80) REVERT: C 90 ASP cc_start: 0.5493 (t0) cc_final: 0.5283 (t0) REVERT: C 105 ASP cc_start: 0.7528 (p0) cc_final: 0.7289 (p0) REVERT: C 151 ARG cc_start: 0.7118 (ttm110) cc_final: 0.6901 (ttm110) REVERT: C 170 MET cc_start: 0.7342 (tpt) cc_final: 0.7087 (tpt) REVERT: C 229 ASP cc_start: 0.7817 (m-30) cc_final: 0.7403 (m-30) REVERT: C 240 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6384 (mpp) outliers start: 16 outliers final: 10 residues processed: 158 average time/residue: 0.1988 time to fit residues: 41.1242 Evaluate side-chains 144 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 LYS 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 49 LEU Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 234 SER 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 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 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 = 0.4156 r_free = 0.4156 target = 0.186167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160626 restraints weight = 6952.619| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.44 r_work: 0.3755 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.6186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7026 Z= 0.269 Angle : 0.651 10.242 9465 Z= 0.316 Chirality : 0.042 0.138 957 Planarity : 0.005 0.042 1044 Dihedral : 20.155 177.370 1953 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.76 % Allowed : 19.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 714 helix: 1.05 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.18 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 42 HIS 0.004 0.001 HIS B 225 PHE 0.025 0.002 PHE A 144 TYR 0.036 0.002 TYR A 81 ARG 0.005 0.001 ARG A 186 *********************** 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 153 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.6898 (mmt) cc_final: 0.6676 (mmt) REVERT: A 175 GLU cc_start: 0.7777 (mp0) cc_final: 0.7539 (mp0) REVERT: A 229 ASP cc_start: 0.8309 (m-30) cc_final: 0.8050 (m-30) REVERT: B 24 LEU cc_start: 0.7439 (tp) cc_final: 0.7215 (tt) REVERT: B 174 LYS cc_start: 0.8367 (ttpp) cc_final: 0.7511 (mttp) REVERT: C 51 MET cc_start: 0.4745 (mtp) cc_final: 0.4208 (ttm) REVERT: C 81 TYR cc_start: 0.7924 (m-80) cc_final: 0.7508 (m-80) REVERT: C 105 ASP cc_start: 0.7782 (p0) cc_final: 0.7531 (p0) REVERT: C 151 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7199 (ttm110) REVERT: C 170 MET cc_start: 0.7225 (tpt) cc_final: 0.6856 (tpt) REVERT: C 240 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6454 (mpp) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.1880 time to fit residues: 37.1671 Evaluate side-chains 138 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 109 THR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 234 SER 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 10 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4207 r_free = 0.4207 target = 0.191331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.165686 restraints weight = 6766.494| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.45 r_work: 0.3790 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7026 Z= 0.203 Angle : 0.601 9.454 9465 Z= 0.294 Chirality : 0.040 0.114 957 Planarity : 0.005 0.042 1044 Dihedral : 18.629 159.281 1953 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.95 % Allowed : 22.28 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.31), residues: 714 helix: 1.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.02 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 42 HIS 0.003 0.001 HIS B 225 PHE 0.025 0.002 PHE A 144 TYR 0.038 0.002 TYR A 81 ARG 0.006 0.000 ARG A 186 *********************** 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 149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7890 (ttpp) REVERT: A 175 GLU cc_start: 0.7834 (mp0) cc_final: 0.7602 (mp0) REVERT: A 229 ASP cc_start: 0.8215 (m-30) cc_final: 0.7990 (m-30) REVERT: B 174 LYS cc_start: 0.8260 (ttpp) cc_final: 0.7370 (mttp) REVERT: B 209 SER cc_start: 0.8258 (p) cc_final: 0.7996 (m) REVERT: C 51 MET cc_start: 0.4841 (mtp) cc_final: 0.4179 (ttm) REVERT: C 81 TYR cc_start: 0.7926 (m-80) cc_final: 0.7666 (m-80) REVERT: C 105 ASP cc_start: 0.7597 (p0) cc_final: 0.7391 (p0) REVERT: C 134 PHE cc_start: 0.8291 (t80) cc_final: 0.8048 (t80) REVERT: C 151 ARG cc_start: 0.7445 (ttm110) cc_final: 0.7161 (ttm110) REVERT: C 170 MET cc_start: 0.7047 (tpt) cc_final: 0.6680 (tpt) REVERT: C 240 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6424 (mpp) REVERT: C 249 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7083 (tt0) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 0.1756 time to fit residues: 34.3966 Evaluate side-chains 140 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 234 SER 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 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.0020 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4206 r_free = 0.4206 target = 0.191146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165358 restraints weight = 6814.683| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.46 r_work: 0.3792 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7026 Z= 0.210 Angle : 0.614 9.093 9465 Z= 0.299 Chirality : 0.040 0.116 957 Planarity : 0.005 0.042 1044 Dihedral : 17.995 154.645 1953 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.63 % Allowed : 22.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 714 helix: 1.27 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 199 HIS 0.002 0.001 HIS C 250 PHE 0.028 0.002 PHE A 144 TYR 0.036 0.002 TYR A 81 ARG 0.006 0.000 ARG A 186 *********************** 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 147 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7813 (ttpp) REVERT: A 175 GLU cc_start: 0.7655 (mp0) cc_final: 0.7407 (mp0) REVERT: A 229 ASP cc_start: 0.8265 (m-30) cc_final: 0.7955 (m-30) REVERT: B 104 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7174 (tt) REVERT: B 174 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7430 (mttp) REVERT: B 209 SER cc_start: 0.8299 (p) cc_final: 0.7999 (m) REVERT: C 51 MET cc_start: 0.4807 (mtp) cc_final: 0.4119 (ttm) REVERT: C 81 TYR cc_start: 0.7910 (m-80) cc_final: 0.7667 (m-80) REVERT: C 134 PHE cc_start: 0.8318 (t80) cc_final: 0.8106 (t80) REVERT: C 151 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7327 (ttm110) outliers start: 10 outliers final: 8 residues processed: 143 average time/residue: 0.1681 time to fit residues: 32.9432 Evaluate side-chains 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 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 184 CYS Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 234 SER 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 15 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.4202 r_free = 0.4202 target = 0.190718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164765 restraints weight = 6891.547| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.47 r_work: 0.3784 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7026 Z= 0.226 Angle : 0.623 9.591 9465 Z= 0.306 Chirality : 0.041 0.126 957 Planarity : 0.005 0.039 1044 Dihedral : 17.400 178.572 1953 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.14 % Allowed : 23.09 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.31), residues: 714 helix: 1.22 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 199 HIS 0.003 0.001 HIS B 172 PHE 0.029 0.002 PHE A 144 TYR 0.033 0.002 TYR A 81 ARG 0.006 0.000 ARG A 186 *********************** 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 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7521 (mp0) cc_final: 0.7278 (mp0) REVERT: B 24 LEU cc_start: 0.7465 (tp) cc_final: 0.7253 (tt) REVERT: B 104 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7093 (tt) REVERT: B 174 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7424 (mttp) REVERT: B 209 SER cc_start: 0.8264 (p) cc_final: 0.8004 (m) REVERT: C 51 MET cc_start: 0.5034 (mtp) cc_final: 0.4366 (ttm) REVERT: C 151 ARG cc_start: 0.7743 (ttm110) cc_final: 0.7491 (ttm110) REVERT: C 249 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7122 (mt-10) outliers start: 7 outliers final: 6 residues processed: 136 average time/residue: 0.1887 time to fit residues: 34.4168 Evaluate side-chains 134 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 234 SER 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 65 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.190298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164230 restraints weight = 6937.372| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.47 r_work: 0.3779 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7026 Z= 0.236 Angle : 0.632 9.818 9465 Z= 0.313 Chirality : 0.042 0.129 957 Planarity : 0.005 0.038 1044 Dihedral : 16.917 161.858 1953 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.14 % Allowed : 23.58 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.31), residues: 714 helix: 1.16 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.85 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 199 HIS 0.006 0.001 HIS C 225 PHE 0.029 0.002 PHE A 144 TYR 0.033 0.002 TYR A 81 ARG 0.005 0.000 ARG A 186 ********************** 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 134 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7702 (mp) cc_final: 0.7252 (mp) REVERT: A 175 GLU cc_start: 0.7521 (mp0) cc_final: 0.7299 (mp0) REVERT: A 229 ASP cc_start: 0.8007 (m-30) cc_final: 0.7687 (m-30) REVERT: B 24 LEU cc_start: 0.7517 (tp) cc_final: 0.7306 (tt) REVERT: B 104 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7106 (tt) REVERT: B 174 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7450 (mttp) REVERT: B 209 SER cc_start: 0.8261 (p) cc_final: 0.7999 (m) REVERT: C 51 MET cc_start: 0.5080 (mtp) cc_final: 0.4403 (ttm) REVERT: C 81 TYR cc_start: 0.7861 (m-80) cc_final: 0.7456 (m-80) REVERT: C 151 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7489 (ttm110) REVERT: C 249 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7099 (mt-10) outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 0.1811 time to fit residues: 32.2449 Evaluate side-chains 131 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 234 SER 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 9 optimal weight: 0.0770 chunk 41 optimal weight: 0.4980 chunk 4 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.194286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168268 restraints weight = 6859.322| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.50 r_work: 0.3827 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7026 Z= 0.196 Angle : 0.602 9.637 9465 Z= 0.301 Chirality : 0.040 0.125 957 Planarity : 0.005 0.040 1044 Dihedral : 16.205 151.733 1953 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.30 % Allowed : 23.09 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 714 helix: 1.21 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.78 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 199 HIS 0.006 0.001 HIS C 225 PHE 0.036 0.002 PHE C 236 TYR 0.032 0.002 TYR A 81 ARG 0.005 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3179.76 seconds wall clock time: 55 minutes 39.73 seconds (3339.73 seconds total)