Starting phenix.real_space_refine on Mon Apr 28 02:29:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdd_45468/04_2025/9cdd_45468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdd_45468/04_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_45468/04_2025/9cdd_45468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdd_45468/04_2025/9cdd_45468.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdd_45468/04_2025/9cdd_45468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdd_45468/04_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-5669/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: 4.36, per 1000 atoms: 0.63 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: 1.98 Conformation dependent library (CDL) restraints added in 819.8 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: 0.51 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: 1.58 Time building geometry restraints manager: 2.26 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: 1.170 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.590 Find NCS groups from input model: 0.120 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- 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 : 0.014 0.478 7032 Z= 1.102 Angle : 1.210 13.948 9465 Z= 0.463 Chirality : 0.085 0.430 957 Planarity : 0.005 0.046 1044 Dihedral : 25.461 172.369 3213 Min Nonbonded Distance : 0.629 Molprobity Statistics. All-atom Clashscore : 22.39 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 Details of bonding type rmsd hydrogen bonds : bond 0.25592 ( 372) hydrogen bonds : angle 7.46603 ( 1116) covalent geometry : bond 0.00933 ( 7026) covalent geometry : angle 1.20987 ( 9465) Misc. bond : bond 0.34311 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 0.617 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: 0.1864 time to fit residues: 46.0235 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 : 0.683 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9980 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: 0.3758 ------------------------------------------------------------------------------- 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 ** 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 = 0.4291 r_free = 0.4291 target = 0.198174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.174675 restraints weight = 6777.082| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.37 r_work: 0.3902 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.249 7032 Z= 0.435 Angle : 1.539 45.874 9465 Z= 0.808 Chirality : 0.077 0.861 957 Planarity : 0.015 0.106 1044 Dihedral : 29.374 174.407 1964 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.39 % Allowed : 13.50 % Favored : 82.11 % 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: -2.98 (0.27), residues: 714 helix: -1.49 (0.20), residues: 504 sheet: None (None), residues: 0 loop : -2.85 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.009 TRP B 138 HIS 0.107 0.014 HIS B 225 PHE 0.223 0.009 PHE C 189 TYR 0.186 0.010 TYR C 177 ARG 0.022 0.003 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.08975 ( 372) hydrogen bonds : angle 6.30585 ( 1116) covalent geometry : bond 0.01062 ( 7026) covalent geometry : angle 1.53902 ( 9465) Misc. bond : bond 0.00221 ( 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 169 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7385 (mm) cc_final: 0.6931 (mm) REVERT: A 51 MET cc_start: 0.3577 (mtt) cc_final: 0.3220 (mtm) REVERT: A 187 TRP cc_start: 0.7093 (m100) cc_final: 0.6605 (m100) REVERT: B 51 MET cc_start: 0.4221 (mtt) cc_final: 0.3787 (ttm) REVERT: B 235 ILE cc_start: 0.7551 (mt) cc_final: 0.7279 (mt) REVERT: C 35 PHE cc_start: 0.7432 (t80) cc_final: 0.6896 (t80) REVERT: C 51 MET cc_start: 0.4397 (mtp) cc_final: 0.3908 (tpt) REVERT: C 129 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6612 (m-10) REVERT: C 224 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6152 (mt) REVERT: C 235 ILE cc_start: 0.6965 (mm) cc_final: 0.6678 (mm) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 0.1781 time to fit residues: 39.2754 Evaluate side-chains 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 216 ILE 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 169 LEU Chi-restraints excluded: chain B residue 176 ARG Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 177 TYR 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: 0.6980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 7.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN ** 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 = 0.4259 r_free = 0.4259 target = 0.195229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170613 restraints weight = 6863.892| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.44 r_work: 0.3854 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7032 Z= 0.161 Angle : 0.643 10.169 9465 Z= 0.312 Chirality : 0.041 0.129 957 Planarity : 0.005 0.043 1044 Dihedral : 25.815 176.736 1964 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.93 % Allowed : 15.93 % Favored : 81.14 % 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: -0.62 (0.30), residues: 714 helix: 0.15 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.66 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 42 HIS 0.006 0.001 HIS B 125 PHE 0.022 0.002 PHE B 195 TYR 0.022 0.002 TYR A 81 ARG 0.004 0.001 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 372) hydrogen bonds : angle 4.85467 ( 1116) covalent geometry : bond 0.00383 ( 7026) covalent geometry : angle 0.64272 ( 9465) Misc. bond : bond 0.00032 ( 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 166 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.3506 (mtt) cc_final: 0.3128 (mtm) REVERT: B 47 LEU cc_start: 0.7918 (tp) cc_final: 0.7676 (tp) REVERT: B 51 MET cc_start: 0.4358 (mtt) cc_final: 0.3639 (ttm) REVERT: B 171 ARG cc_start: 0.6604 (mtm110) cc_final: 0.6052 (mtm110) REVERT: B 240 MET cc_start: 0.7318 (tpp) cc_final: 0.6990 (tpp) REVERT: C 81 TYR cc_start: 0.7797 (m-80) cc_final: 0.7173 (m-80) REVERT: C 172 HIS cc_start: 0.6403 (m170) cc_final: 0.6151 (m170) REVERT: C 229 ASP cc_start: 0.7811 (m-30) cc_final: 0.7477 (m-30) REVERT: C 235 ILE cc_start: 0.7108 (mm) cc_final: 0.6846 (mm) REVERT: C 240 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6579 (mpp) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 0.1783 time to fit residues: 37.7349 Evaluate side-chains 135 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 109 THR Chi-restraints excluded: chain B residue 160 CYS 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: 1.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** C 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.189406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165278 restraints weight = 7007.379| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.40 r_work: 0.3799 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7032 Z= 0.168 Angle : 0.651 10.791 9465 Z= 0.316 Chirality : 0.042 0.178 957 Planarity : 0.005 0.038 1044 Dihedral : 22.744 176.278 1954 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.76 % Allowed : 16.26 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.31), residues: 714 helix: 0.67 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.23 (0.45), 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 0.033 0.002 PHE C 134 TYR 0.050 0.002 TYR A 81 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 372) hydrogen bonds : angle 4.69833 ( 1116) covalent geometry : bond 0.00401 ( 7026) covalent geometry : angle 0.65143 ( 9465) Misc. bond : bond 0.00017 ( 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 154 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: A 187 TRP cc_start: 0.7139 (m100) cc_final: 0.6916 (m100) REVERT: A 189 PHE cc_start: 0.7004 (t80) cc_final: 0.6753 (t80) REVERT: B 51 MET cc_start: 0.5343 (mtt) cc_final: 0.4363 (ttm) REVERT: B 105 ASP cc_start: 0.7886 (p0) cc_final: 0.7457 (p0) REVERT: B 186 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6605 (ptm160) REVERT: B 218 GLN cc_start: 0.5378 (tt0) cc_final: 0.4300 (tp-100) REVERT: C 235 ILE cc_start: 0.7157 (mm) cc_final: 0.6894 (mm) REVERT: C 240 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6632 (mpp) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.2019 time to fit residues: 40.1410 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 : 0.734 ------------------------------------------------------------------------------- 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 125 HIS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 231 THR 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 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: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.189229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.164116 restraints weight = 6839.584| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.44 r_work: 0.3793 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7032 Z= 0.163 Angle : 0.621 8.402 9465 Z= 0.302 Chirality : 0.041 0.134 957 Planarity : 0.005 0.038 1044 Dihedral : 21.325 176.113 1953 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.76 % Allowed : 18.21 % Favored : 79.02 % 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: 0.47 (0.31), residues: 714 helix: 0.98 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 207 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 0.026 0.002 PHE C 189 TYR 0.037 0.002 TYR A 81 ARG 0.007 0.001 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 372) hydrogen bonds : angle 4.57974 ( 1116) covalent geometry : bond 0.00390 ( 7026) covalent geometry : angle 0.62145 ( 9465) Misc. bond : bond 0.00030 ( 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 156 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: A 187 TRP cc_start: 0.6982 (m100) cc_final: 0.6777 (m100) REVERT: A 229 ASP cc_start: 0.8277 (m-30) cc_final: 0.8016 (m-30) REVERT: B 51 MET cc_start: 0.5777 (mtt) cc_final: 0.5548 (mtm) REVERT: B 105 ASP cc_start: 0.7646 (p0) cc_final: 0.7443 (p0) REVERT: B 174 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7309 (mttp) REVERT: B 199 TRP cc_start: 0.6834 (m100) cc_final: 0.6601 (m100) REVERT: C 81 TYR cc_start: 0.7893 (m-80) cc_final: 0.7539 (m-80) REVERT: C 171 ARG cc_start: 0.7804 (tmt170) cc_final: 0.7138 (ttp80) REVERT: C 240 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6477 (mpp) REVERT: C 249 GLU cc_start: 0.7635 (tt0) cc_final: 0.7416 (tt0) outliers start: 17 outliers final: 11 residues processed: 149 average time/residue: 0.2274 time to fit residues: 45.1415 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 : 1.368 ------------------------------------------------------------------------------- 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 125 HIS 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 160 CYS 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: 0.8980 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS ** C 172 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 = 0.4180 r_free = 0.4180 target = 0.188799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163770 restraints weight = 6917.465| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.44 r_work: 0.3779 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7032 Z= 0.157 Angle : 0.620 9.986 9465 Z= 0.300 Chirality : 0.041 0.123 957 Planarity : 0.005 0.039 1044 Dihedral : 19.836 173.999 1953 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.76 % Allowed : 20.00 % Favored : 77.24 % 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: 0.71 (0.31), residues: 714 helix: 1.11 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.12 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.004 0.001 HIS A 225 PHE 0.029 0.002 PHE C 189 TYR 0.033 0.002 TYR A 81 ARG 0.006 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 372) hydrogen bonds : angle 4.47831 ( 1116) covalent geometry : bond 0.00379 ( 7026) covalent geometry : angle 0.61955 ( 9465) Misc. bond : bond 0.00016 ( 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 153 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: A 162 PHE cc_start: 0.7375 (t80) cc_final: 0.7114 (t80) REVERT: A 229 ASP cc_start: 0.8262 (m-30) cc_final: 0.8048 (m-30) REVERT: A 240 MET cc_start: 0.6699 (mtp) cc_final: 0.6484 (mtm) REVERT: B 43 MET cc_start: 0.7380 (ptm) cc_final: 0.6930 (ptp) REVERT: B 51 MET cc_start: 0.5911 (mtt) cc_final: 0.5598 (mtm) REVERT: B 174 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7319 (mttp) REVERT: B 209 SER cc_start: 0.8387 (p) cc_final: 0.8092 (m) REVERT: B 230 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6082 (tp) REVERT: C 81 TYR cc_start: 0.7973 (m-80) cc_final: 0.7584 (m-80) REVERT: C 151 ARG cc_start: 0.7461 (ttm110) cc_final: 0.7240 (ttm110) REVERT: C 240 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6545 (mpp) REVERT: C 249 GLU cc_start: 0.7773 (tt0) cc_final: 0.7572 (tt0) outliers start: 17 outliers final: 12 residues processed: 149 average time/residue: 0.2144 time to fit residues: 42.8480 Evaluate side-chains 142 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 125 HIS 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 184 CYS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 THR 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 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: 0.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.189629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164452 restraints weight = 6771.785| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.43 r_work: 0.3791 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7032 Z= 0.149 Angle : 0.609 8.550 9465 Z= 0.296 Chirality : 0.041 0.128 957 Planarity : 0.005 0.038 1044 Dihedral : 18.701 162.099 1953 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.76 % Allowed : 20.49 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.31), residues: 714 helix: 1.25 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 42 HIS 0.003 0.001 HIS C 172 PHE 0.030 0.002 PHE C 189 TYR 0.025 0.002 TYR A 81 ARG 0.006 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 372) hydrogen bonds : angle 4.48403 ( 1116) covalent geometry : bond 0.00359 ( 7026) covalent geometry : angle 0.60857 ( 9465) Misc. bond : bond 0.00020 ( 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 157 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7375 (t80) cc_final: 0.7089 (t80) REVERT: A 189 PHE cc_start: 0.7301 (t80) cc_final: 0.6885 (t80) REVERT: B 43 MET cc_start: 0.7347 (ptm) cc_final: 0.6906 (ptp) REVERT: B 51 MET cc_start: 0.6146 (mtt) cc_final: 0.5924 (mtm) REVERT: B 174 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7318 (mttp) REVERT: B 209 SER cc_start: 0.8357 (p) cc_final: 0.8048 (m) REVERT: C 81 TYR cc_start: 0.7981 (m-80) cc_final: 0.7723 (m-80) REVERT: C 151 ARG cc_start: 0.7441 (ttm110) cc_final: 0.7202 (ttm110) REVERT: C 235 ILE cc_start: 0.7216 (mm) cc_final: 0.6969 (mm) REVERT: C 240 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6423 (mpp) REVERT: C 249 GLU cc_start: 0.7666 (tt0) cc_final: 0.7431 (tt0) outliers start: 17 outliers final: 13 residues processed: 150 average time/residue: 0.2753 time to fit residues: 54.7743 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 : 1.887 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS 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 47 LEU 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: 0.9980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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** ** C 172 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 = 0.4192 r_free = 0.4192 target = 0.190110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164549 restraints weight = 6788.140| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.43 r_work: 0.3789 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.6799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.147 Angle : 0.612 8.268 9465 Z= 0.299 Chirality : 0.041 0.121 957 Planarity : 0.005 0.039 1044 Dihedral : 18.124 169.593 1953 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 20.81 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.31), residues: 714 helix: 1.20 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 199 HIS 0.002 0.001 HIS B 125 PHE 0.035 0.002 PHE C 236 TYR 0.026 0.002 TYR A 45 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 372) hydrogen bonds : angle 4.50651 ( 1116) covalent geometry : bond 0.00351 ( 7026) covalent geometry : angle 0.61231 ( 9465) Misc. bond : bond 0.00018 ( 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 145 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7359 (t80) cc_final: 0.7073 (t80) REVERT: B 43 MET cc_start: 0.7379 (ptm) cc_final: 0.6975 (ptp) REVERT: B 51 MET cc_start: 0.6267 (mtt) cc_final: 0.5904 (mtm) REVERT: B 174 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7368 (mttp) REVERT: B 209 SER cc_start: 0.8355 (p) cc_final: 0.8068 (m) REVERT: C 81 TYR cc_start: 0.7957 (m-80) cc_final: 0.7708 (m-80) REVERT: C 235 ILE cc_start: 0.7216 (mm) cc_final: 0.7010 (mm) REVERT: C 240 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6833 (mpp) REVERT: C 249 GLU cc_start: 0.7630 (tt0) cc_final: 0.7408 (tt0) outliers start: 15 outliers final: 14 residues processed: 139 average time/residue: 0.1954 time to fit residues: 36.7424 Evaluate side-chains 135 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 233 LYS 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 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** C 172 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 = 0.4198 r_free = 0.4198 target = 0.190615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164724 restraints weight = 6851.460| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.45 r_work: 0.3787 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7032 Z= 0.151 Angle : 0.625 8.523 9465 Z= 0.306 Chirality : 0.041 0.131 957 Planarity : 0.005 0.038 1044 Dihedral : 17.553 172.142 1953 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.93 % Allowed : 20.65 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.31), residues: 714 helix: 1.05 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.97 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 199 HIS 0.003 0.001 HIS B 225 PHE 0.037 0.002 PHE C 189 TYR 0.038 0.002 TYR A 81 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 372) hydrogen bonds : angle 4.53747 ( 1116) covalent geometry : bond 0.00361 ( 7026) covalent geometry : angle 0.62474 ( 9465) Misc. bond : bond 0.00019 ( 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 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7407 (t80) cc_final: 0.7073 (t80) REVERT: A 189 PHE cc_start: 0.7231 (t80) cc_final: 0.6893 (t80) REVERT: B 35 PHE cc_start: 0.7479 (t80) cc_final: 0.7101 (t80) REVERT: B 43 MET cc_start: 0.7283 (ptm) cc_final: 0.6837 (ptp) REVERT: B 51 MET cc_start: 0.6416 (mtt) cc_final: 0.6094 (mtm) REVERT: B 174 LYS cc_start: 0.8044 (ttpp) cc_final: 0.7318 (mttp) REVERT: B 209 SER cc_start: 0.8316 (p) cc_final: 0.8035 (m) REVERT: C 152 PHE cc_start: 0.6601 (m-80) cc_final: 0.6382 (m-80) REVERT: C 235 ILE cc_start: 0.7159 (mm) cc_final: 0.6933 (mm) REVERT: C 240 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6545 (mpp) outliers start: 18 outliers final: 16 residues processed: 130 average time/residue: 0.1692 time to fit residues: 30.0126 Evaluate side-chains 130 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 233 LYS 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 170 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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** ** C 172 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 = 0.4204 r_free = 0.4204 target = 0.191658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165347 restraints weight = 6872.595| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.47 r_work: 0.3799 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.7133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7032 Z= 0.143 Angle : 0.619 8.535 9465 Z= 0.304 Chirality : 0.041 0.133 957 Planarity : 0.005 0.038 1044 Dihedral : 16.907 162.377 1953 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 21.30 % 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: 0.80 (0.31), residues: 714 helix: 1.08 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.86 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 199 HIS 0.003 0.001 HIS B 225 PHE 0.040 0.002 PHE C 189 TYR 0.036 0.002 TYR A 81 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 372) hydrogen bonds : angle 4.54792 ( 1116) covalent geometry : bond 0.00339 ( 7026) covalent geometry : angle 0.61891 ( 9465) Misc. bond : bond 0.00021 ( 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 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7382 (t80) cc_final: 0.7049 (t80) REVERT: A 174 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7628 (mmtt) REVERT: A 189 PHE cc_start: 0.7200 (t80) cc_final: 0.6859 (t80) REVERT: B 35 PHE cc_start: 0.7472 (t80) cc_final: 0.7187 (t80) REVERT: B 43 MET cc_start: 0.7253 (ptm) cc_final: 0.6799 (ptp) REVERT: B 51 MET cc_start: 0.6347 (mtt) cc_final: 0.6001 (mtm) REVERT: B 104 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7124 (tt) REVERT: B 174 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7355 (mttp) REVERT: B 187 TRP cc_start: 0.7009 (m100) cc_final: 0.6774 (m100) REVERT: B 209 SER cc_start: 0.8219 (p) cc_final: 0.8008 (m) REVERT: C 81 TYR cc_start: 0.7930 (m-80) cc_final: 0.7415 (m-80) REVERT: C 240 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6558 (mpp) REVERT: C 249 GLU cc_start: 0.7101 (tt0) cc_final: 0.6877 (mt-10) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.1937 time to fit residues: 34.6744 Evaluate side-chains 135 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 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 49 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 233 LYS 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 234 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 253 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** 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 = 0.4199 r_free = 0.4199 target = 0.191085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165355 restraints weight = 6853.978| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.46 r_work: 0.3790 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.150 Angle : 0.631 8.815 9465 Z= 0.310 Chirality : 0.041 0.136 957 Planarity : 0.005 0.038 1044 Dihedral : 16.439 153.309 1953 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.44 % Allowed : 21.14 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.31), residues: 714 helix: 1.12 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.71 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 199 HIS 0.003 0.001 HIS B 225 PHE 0.040 0.002 PHE C 189 TYR 0.036 0.002 TYR A 81 ARG 0.008 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 372) hydrogen bonds : angle 4.54504 ( 1116) covalent geometry : bond 0.00357 ( 7026) covalent geometry : angle 0.63124 ( 9465) Misc. bond : bond 0.00037 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.31 seconds wall clock time: 70 minutes 32.86 seconds (4232.86 seconds total)