Starting phenix.real_space_refine on Sat May 10 20:39:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdd_45468/05_2025/9cdd_45468_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdd_45468/05_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_45468/05_2025/9cdd_45468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdd_45468/05_2025/9cdd_45468.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdd_45468/05_2025/9cdd_45468_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdd_45468/05_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-5687/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: 4.52, per 1000 atoms: 0.66 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: 2.16 Conformation dependent library (CDL) restraints added in 873.6 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: 0.57 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: 1.82 Time building geometry restraints manager: 2.40 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: 1.040 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.170 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- 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 : 0.602 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: 0.1795 time to fit residues: 44.0963 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 : 0.652 ------------------------------------------------------------------------------- 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 = 0.174677 restraints weight = 6777.084| |-----------------------------------------------------------------------------| 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: 0.6545 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 45.875 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 1.53903 ( 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 : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ILE cc_start: 0.7384 (mm) cc_final: 0.6931 (mm) REVERT: A 51 MET cc_start: 0.3568 (mtt) cc_final: 0.3210 (mtm) REVERT: A 187 TRP cc_start: 0.7094 (m100) cc_final: 0.6604 (m100) REVERT: B 51 MET cc_start: 0.4227 (mtt) cc_final: 0.3787 (ttm) REVERT: B 235 ILE cc_start: 0.7552 (mt) cc_final: 0.7280 (mt) REVERT: C 35 PHE cc_start: 0.7434 (t80) cc_final: 0.6900 (t80) REVERT: C 51 MET cc_start: 0.4395 (mtp) cc_final: 0.3898 (tpt) REVERT: C 129 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: C 224 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6150 (mt) REVERT: C 235 ILE cc_start: 0.6965 (mm) cc_final: 0.6679 (mm) outliers start: 27 outliers final: 15 residues processed: 164 average time/residue: 0.1783 time to fit residues: 39.5164 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 : 0.580 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.194717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170064 restraints weight = 6863.636| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.43 r_work: 0.3858 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7032 Z= 0.169 Angle : 0.653 10.026 9465 Z= 0.318 Chirality : 0.041 0.133 957 Planarity : 0.005 0.044 1044 Dihedral : 25.339 176.176 1964 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.74 % Allowed : 15.45 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.30), residues: 714 helix: 0.13 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 42 HIS 0.005 0.001 HIS B 125 PHE 0.023 0.002 PHE B 195 TYR 0.025 0.002 TYR A 81 ARG 0.004 0.001 ARG C 176 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 372) hydrogen bonds : angle 4.84141 ( 1116) covalent geometry : bond 0.00403 ( 7026) covalent geometry : angle 0.65288 ( 9465) Misc. bond : bond 0.00043 ( 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 172 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5303 (m-10) REVERT: B 47 LEU cc_start: 0.8053 (tp) cc_final: 0.7804 (tp) REVERT: B 51 MET cc_start: 0.4343 (mtt) cc_final: 0.3704 (ttm) REVERT: B 171 ARG cc_start: 0.6600 (mtm110) cc_final: 0.6032 (mtm110) REVERT: C 81 TYR cc_start: 0.7697 (m-80) cc_final: 0.7490 (m-80) REVERT: C 172 HIS cc_start: 0.6369 (m170) cc_final: 0.6117 (m170) REVERT: C 229 ASP cc_start: 0.8012 (m-30) cc_final: 0.7544 (m-30) REVERT: C 235 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6887 (mm) REVERT: C 240 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6645 (mpp) outliers start: 23 outliers final: 11 residues processed: 162 average time/residue: 0.1767 time to fit residues: 38.4881 Evaluate side-chains 140 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain C residue 160 CYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 235 ILE 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: 6.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 185 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.187296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163022 restraints weight = 7036.460| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.40 r_work: 0.3774 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7032 Z= 0.184 Angle : 0.671 11.062 9465 Z= 0.325 Chirality : 0.042 0.142 957 Planarity : 0.005 0.041 1044 Dihedral : 22.782 173.035 1954 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.41 % Allowed : 16.75 % Favored : 79.84 % 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: 0.12 (0.31), residues: 714 helix: 0.70 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 42 HIS 0.004 0.001 HIS A 225 PHE 0.035 0.002 PHE C 134 TYR 0.048 0.002 TYR A 81 ARG 0.006 0.001 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04850 ( 372) hydrogen bonds : angle 4.79042 ( 1116) covalent geometry : bond 0.00446 ( 7026) covalent geometry : angle 0.67119 ( 9465) Misc. bond : bond 0.00022 ( 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 163 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.6600 (mmt) cc_final: 0.6394 (mtp) REVERT: A 189 PHE cc_start: 0.7006 (t80) cc_final: 0.6792 (t80) REVERT: A 229 ASP cc_start: 0.8266 (m-30) cc_final: 0.7899 (m-30) REVERT: A 240 MET cc_start: 0.6692 (mtp) cc_final: 0.6481 (mtm) REVERT: B 51 MET cc_start: 0.5505 (mtt) cc_final: 0.4511 (ttm) REVERT: B 105 ASP cc_start: 0.7913 (p0) cc_final: 0.7429 (p0) REVERT: B 174 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7572 (ttmm) REVERT: B 186 ARG cc_start: 0.6823 (ttp-110) cc_final: 0.6581 (ptm160) REVERT: B 218 GLN cc_start: 0.5382 (tt0) cc_final: 0.4311 (tp-100) REVERT: C 235 ILE cc_start: 0.7102 (mm) cc_final: 0.6885 (mm) REVERT: C 240 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6708 (mpp) outliers start: 21 outliers final: 14 residues processed: 157 average time/residue: 0.1988 time to fit residues: 41.0094 Evaluate side-chains 143 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 THR 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 179 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.188981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163949 restraints weight = 6823.905| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.42 r_work: 0.3774 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7032 Z= 0.154 Angle : 0.616 9.965 9465 Z= 0.297 Chirality : 0.041 0.118 957 Planarity : 0.005 0.044 1044 Dihedral : 21.187 179.233 1953 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.28 % Allowed : 18.21 % 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: 0.55 (0.31), residues: 714 helix: 1.01 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.27 (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 C 225 PHE 0.024 0.002 PHE A 144 TYR 0.039 0.002 TYR A 81 ARG 0.007 0.001 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 372) hydrogen bonds : angle 4.62515 ( 1116) covalent geometry : bond 0.00374 ( 7026) covalent geometry : angle 0.61646 ( 9465) Misc. bond : bond 0.00031 ( 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 158 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.6862 (mmt) cc_final: 0.6622 (mtp) REVERT: A 229 ASP cc_start: 0.8222 (m-30) cc_final: 0.7892 (m-30) REVERT: A 240 MET cc_start: 0.6682 (mtp) cc_final: 0.6459 (mtm) REVERT: B 105 ASP cc_start: 0.7810 (p0) cc_final: 0.7521 (p0) REVERT: B 174 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7402 (mttp) REVERT: B 186 ARG cc_start: 0.6992 (ttp-110) cc_final: 0.6679 (ptm160) REVERT: B 209 SER cc_start: 0.8247 (p) cc_final: 0.8017 (m) REVERT: C 229 ASP cc_start: 0.7884 (m-30) cc_final: 0.7495 (m-30) REVERT: C 235 ILE cc_start: 0.7166 (mm) cc_final: 0.6942 (mm) REVERT: C 240 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6433 (mpp) outliers start: 14 outliers final: 11 residues processed: 152 average time/residue: 0.1941 time to fit residues: 38.8147 Evaluate side-chains 142 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 109 THR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 160 CYS 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 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: 0.8980 chunk 62 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.191758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.166465 restraints weight = 6836.284| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.45 r_work: 0.3799 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7032 Z= 0.137 Angle : 0.589 9.696 9465 Z= 0.289 Chirality : 0.040 0.120 957 Planarity : 0.005 0.039 1044 Dihedral : 19.632 165.855 1953 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.11 % Allowed : 20.65 % 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: 0.82 (0.30), residues: 714 helix: 1.20 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 42 HIS 0.003 0.001 HIS A 225 PHE 0.026 0.002 PHE A 144 TYR 0.034 0.002 TYR A 81 ARG 0.005 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 372) hydrogen bonds : angle 4.56336 ( 1116) covalent geometry : bond 0.00324 ( 7026) covalent geometry : angle 0.58917 ( 9465) Misc. bond : bond 0.00018 ( 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 159 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.6397 (pt0) cc_final: 0.5945 (mp0) REVERT: A 189 PHE cc_start: 0.7236 (t80) cc_final: 0.6855 (t80) REVERT: B 150 TYR cc_start: 0.6900 (m-80) cc_final: 0.6570 (m-80) REVERT: B 174 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7367 (mttp) REVERT: B 186 ARG cc_start: 0.6984 (ttp-110) cc_final: 0.6641 (ptm160) REVERT: B 209 SER cc_start: 0.8247 (p) cc_final: 0.7971 (m) REVERT: C 51 MET cc_start: 0.4212 (ptp) cc_final: 0.3935 (ptp) REVERT: C 81 TYR cc_start: 0.7889 (m-80) cc_final: 0.7419 (m-80) REVERT: C 151 ARG cc_start: 0.7449 (ttm110) cc_final: 0.7232 (ttm110) REVERT: C 229 ASP cc_start: 0.7451 (m-30) cc_final: 0.7229 (m-30) REVERT: C 240 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6488 (mpp) outliers start: 13 outliers final: 11 residues processed: 154 average time/residue: 0.2064 time to fit residues: 41.4643 Evaluate side-chains 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 213 THR Chi-restraints excluded: chain B residue 230 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS ** B 225 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 = 0.4169 r_free = 0.4169 target = 0.187164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.161130 restraints weight = 6762.582| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.44 r_work: 0.3745 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.6511 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= 0.173 Angle : 0.648 8.922 9465 Z= 0.312 Chirality : 0.042 0.134 957 Planarity : 0.005 0.037 1044 Dihedral : 18.923 171.582 1953 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.25 % Allowed : 20.81 % Favored : 75.93 % 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: 0.76 (0.30), residues: 714 helix: 1.08 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.92 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 42 HIS 0.005 0.001 HIS A 225 PHE 0.027 0.002 PHE A 144 TYR 0.023 0.002 TYR A 45 ARG 0.006 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 372) hydrogen bonds : angle 4.71190 ( 1116) covalent geometry : bond 0.00422 ( 7026) covalent geometry : angle 0.64796 ( 9465) Misc. bond : bond 0.00014 ( 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 155 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7385 (t80) cc_final: 0.7110 (t80) REVERT: B 24 LEU cc_start: 0.7461 (tp) cc_final: 0.7213 (tt) REVERT: B 150 TYR cc_start: 0.6977 (m-80) cc_final: 0.6558 (m-80) REVERT: B 174 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7402 (mttp) REVERT: B 209 SER cc_start: 0.8272 (p) cc_final: 0.8047 (m) REVERT: C 81 TYR cc_start: 0.7925 (m-80) cc_final: 0.7640 (m-80) REVERT: C 105 ASP cc_start: 0.7655 (p0) cc_final: 0.7062 (p0) REVERT: C 151 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7321 (ttm110) REVERT: C 240 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6399 (mpp) outliers start: 20 outliers final: 16 residues processed: 148 average time/residue: 0.1889 time to fit residues: 37.1975 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 : 0.650 ------------------------------------------------------------------------------- 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 230 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 160 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.189820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164025 restraints weight = 6765.630| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.45 r_work: 0.3773 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7032 Z= 0.153 Angle : 0.626 8.783 9465 Z= 0.306 Chirality : 0.041 0.118 957 Planarity : 0.005 0.038 1044 Dihedral : 18.149 169.413 1953 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 21.14 % 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: 0.97 (0.31), residues: 714 helix: 1.22 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.76 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.002 0.001 HIS B 225 PHE 0.035 0.002 PHE C 236 TYR 0.029 0.002 TYR A 81 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04487 ( 372) hydrogen bonds : angle 4.64488 ( 1116) covalent geometry : bond 0.00365 ( 7026) covalent geometry : angle 0.62560 ( 9465) Misc. bond : bond 0.00012 ( 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 146 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7347 (t80) cc_final: 0.7090 (t80) REVERT: A 189 PHE cc_start: 0.7340 (t80) cc_final: 0.6949 (t80) REVERT: B 24 LEU cc_start: 0.7484 (tp) cc_final: 0.7235 (tt) REVERT: B 150 TYR cc_start: 0.6929 (m-80) cc_final: 0.6497 (m-80) REVERT: B 174 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7444 (mttp) REVERT: B 209 SER cc_start: 0.8229 (p) cc_final: 0.7978 (m) REVERT: C 81 TYR cc_start: 0.7936 (m-80) cc_final: 0.7634 (m-80) REVERT: C 105 ASP cc_start: 0.7550 (p0) cc_final: 0.7181 (p0) REVERT: C 151 ARG cc_start: 0.7670 (ttm110) cc_final: 0.7438 (ttm110) REVERT: C 229 ASP cc_start: 0.7839 (m-30) cc_final: 0.7533 (m-30) REVERT: C 240 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6886 (mpp) outliers start: 19 outliers final: 15 residues processed: 139 average time/residue: 0.1885 time to fit residues: 34.9411 Evaluate side-chains 137 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 230 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 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 = 0.4210 r_free = 0.4210 target = 0.191808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166058 restraints weight = 6807.584| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.46 r_work: 0.3790 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.6985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7032 Z= 0.139 Angle : 0.604 8.723 9465 Z= 0.297 Chirality : 0.041 0.124 957 Planarity : 0.005 0.037 1044 Dihedral : 17.321 176.126 1953 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 21.63 % Favored : 75.93 % 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: 1.08 (0.31), residues: 714 helix: 1.30 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -0.71 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 210 HIS 0.002 0.001 HIS B 250 PHE 0.033 0.002 PHE C 236 TYR 0.029 0.002 TYR A 81 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 372) hydrogen bonds : angle 4.57637 ( 1116) covalent geometry : bond 0.00326 ( 7026) covalent geometry : angle 0.60379 ( 9465) Misc. bond : bond 0.00013 ( 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 149 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7360 (t80) cc_final: 0.7078 (t80) REVERT: A 189 PHE cc_start: 0.7286 (t80) cc_final: 0.6897 (t80) REVERT: B 81 TYR cc_start: 0.7527 (m-80) cc_final: 0.7026 (m-80) REVERT: B 150 TYR cc_start: 0.6944 (m-80) cc_final: 0.6560 (m-80) REVERT: B 174 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7460 (mttp) REVERT: C 81 TYR cc_start: 0.7823 (m-80) cc_final: 0.7621 (m-80) REVERT: C 105 ASP cc_start: 0.7319 (p0) cc_final: 0.6993 (p0) REVERT: C 151 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7402 (ttm110) REVERT: C 229 ASP cc_start: 0.7740 (m-30) cc_final: 0.7404 (m-30) REVERT: C 240 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6584 (mpp) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 0.1729 time to fit residues: 33.6845 Evaluate side-chains 138 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 213 THR Chi-restraints excluded: chain B residue 230 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** 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 = 0.4190 r_free = 0.4190 target = 0.189818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.163829 restraints weight = 6900.981| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.47 r_work: 0.3772 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7032 Z= 0.159 Angle : 0.645 9.096 9465 Z= 0.317 Chirality : 0.042 0.115 957 Planarity : 0.005 0.037 1044 Dihedral : 16.893 157.059 1953 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.44 % Allowed : 21.46 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.31), residues: 714 helix: 1.23 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.75 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 42 HIS 0.002 0.001 HIS B 225 PHE 0.030 0.002 PHE A 144 TYR 0.027 0.002 TYR A 81 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04580 ( 372) hydrogen bonds : angle 4.66037 ( 1116) covalent geometry : bond 0.00387 ( 7026) covalent geometry : angle 0.64513 ( 9465) Misc. bond : bond 0.00016 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.7372 (t80) cc_final: 0.7059 (t80) REVERT: A 174 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7642 (mmtt) REVERT: B 81 TYR cc_start: 0.7386 (m-80) cc_final: 0.6954 (m-80) REVERT: B 104 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7246 (tt) REVERT: B 106 TYR cc_start: 0.7157 (m-10) cc_final: 0.6699 (m-80) REVERT: B 150 TYR cc_start: 0.6956 (m-80) cc_final: 0.6555 (m-80) REVERT: B 174 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7427 (mttp) REVERT: C 151 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7508 (ttm110) REVERT: C 167 LEU cc_start: 0.7195 (mt) cc_final: 0.6884 (tp) REVERT: C 229 ASP cc_start: 0.7801 (m-30) cc_final: 0.7543 (m-30) REVERT: C 240 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6648 (mpp) outliers start: 15 outliers final: 11 residues processed: 140 average time/residue: 0.1783 time to fit residues: 33.3427 Evaluate side-chains 138 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 230 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** C 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.190242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164334 restraints weight = 6862.377| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.47 r_work: 0.3788 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7032 Z= 0.153 Angle : 0.641 8.597 9465 Z= 0.317 Chirality : 0.042 0.145 957 Planarity : 0.005 0.036 1044 Dihedral : 16.500 144.948 1953 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.76 % Allowed : 21.30 % Favored : 75.93 % 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: 1.01 (0.31), residues: 714 helix: 1.20 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -0.61 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 210 HIS 0.002 0.001 HIS B 225 PHE 0.029 0.002 PHE A 144 TYR 0.026 0.002 TYR A 45 ARG 0.007 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 372) hydrogen bonds : angle 4.68685 ( 1116) covalent geometry : bond 0.00368 ( 7026) covalent geometry : angle 0.64050 ( 9465) Misc. bond : bond 0.00018 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.06 seconds wall clock time: 59 minutes 16.60 seconds (3556.60 seconds total)