Starting phenix.real_space_refine on Tue Aug 4 23:46:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.map" model { file = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2026/8okd_16926.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.058 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 138 5.49 5 S 30 5.16 5 C 4392 2.51 5 N 1358 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2390 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2390 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 2 Chain: "C" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1484 Classifications: {'RNA': 70} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain breaks: 1 Chain: "X" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1484 Classifications: {'RNA': 70} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 58} Chain breaks: 1 Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7748 At special positions: 0 Unit cell: (98.9, 162.54, 66.22, 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 30 16.00 P 138 15.00 O 1830 8.00 N 1358 7.00 C 4392 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=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 278.7 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 37.3% alpha, 21.0% beta 46 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.782A pdb=" N ALA A 59 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.718A pdb=" N LYS A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.954A pdb=" N SER A 109 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.862A pdb=" N VAL A 217 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.746A pdb=" N CYS A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 removed outlier: 4.281A pdb=" N GLU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 337 through 369 removed outlier: 3.842A pdb=" N LYS A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.909A pdb=" N ALA B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.827A pdb=" N LYS B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 4.038A pdb=" N SER B 109 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 166 removed outlier: 3.660A pdb=" N ARG B 166 " --> pdb=" O HIS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.731A pdb=" N CYS B 281 " --> pdb=" O HIS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 304 removed outlier: 4.333A pdb=" N GLU B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 369 removed outlier: 3.801A pdb=" N LYS B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.762A pdb=" N SER A 129 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 128 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.762A pdb=" N SER A 129 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 128 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 removed outlier: 7.098A pdb=" N SER A 122 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP A 326 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A 194 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 243 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.531A pdb=" N GLY A 218 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 241 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 239 " --> pdb=" O HIS A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 134 removed outlier: 7.798A pdb=" N HIS B 64 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 66 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP B 177 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ARG B 68 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 removed outlier: 6.824A pdb=" N SER B 122 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP B 326 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR B 194 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 269 " --> pdb=" O TYR B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221 190 hydrogen bonds defined for protein. 507 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1941 1.34 - 1.46: 2451 1.46 - 1.57: 3492 1.57 - 1.69: 274 1.69 - 1.81: 48 Bond restraints: 8206 Sorted by residual: bond pdb=" C GLU A 260 " pdb=" N PRO A 261 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.75e+00 bond pdb=" C GLU B 260 " pdb=" N PRO B 261 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.68e+00 bond pdb=" C2 U C 39 " pdb=" N3 U C 39 " ideal model delta sigma weight residual 1.373 1.364 0.009 7.00e-03 2.04e+04 1.53e+00 bond pdb=" N9 A C 24 " pdb=" C4 A C 24 " ideal model delta sigma weight residual 1.374 1.367 0.007 6.00e-03 2.78e+04 1.23e+00 bond pdb=" N9 A C 21 " pdb=" C4 A C 21 " ideal model delta sigma weight residual 1.374 1.367 0.007 6.00e-03 2.78e+04 1.22e+00 ... (remaining 8201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11203 1.66 - 3.31: 536 3.31 - 4.97: 21 4.97 - 6.63: 3 6.63 - 8.28: 3 Bond angle restraints: 11766 Sorted by residual: angle pdb=" O5' G X 18 " pdb=" C5' G X 18 " pdb=" C4' G X 18 " ideal model delta sigma weight residual 109.40 112.41 -3.01 8.00e-01 1.56e+00 1.42e+01 angle pdb=" O5' U C 16 " pdb=" C5' U C 16 " pdb=" C4' U C 16 " ideal model delta sigma weight residual 109.40 112.37 -2.97 8.00e-01 1.56e+00 1.37e+01 angle pdb=" O5' G X 17 " pdb=" C5' G X 17 " pdb=" C4' G X 17 " ideal model delta sigma weight residual 109.40 112.28 -2.88 8.00e-01 1.56e+00 1.29e+01 angle pdb=" O5' U C 20 " pdb=" C5' U C 20 " pdb=" C4' U C 20 " ideal model delta sigma weight residual 109.40 112.25 -2.85 8.00e-01 1.56e+00 1.27e+01 angle pdb=" O5' A X 57 " pdb=" C5' A X 57 " pdb=" C4' A X 57 " ideal model delta sigma weight residual 109.40 112.19 -2.79 8.00e-01 1.56e+00 1.22e+01 ... (remaining 11761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.81: 4606 32.81 - 65.63: 431 65.63 - 98.44: 58 98.44 - 131.25: 2 131.25 - 164.07: 1 Dihedral angle restraints: 5098 sinusoidal: 3384 harmonic: 1714 Sorted by residual: dihedral pdb=" O4' C X 48 " pdb=" C1' C X 48 " pdb=" N1 C X 48 " pdb=" C2 C X 48 " ideal model delta sinusoidal sigma weight residual -160.00 -54.00 -106.00 1 1.50e+01 4.44e-03 5.44e+01 dihedral pdb=" O4' C C 48 " pdb=" C1' C C 48 " pdb=" N1 C C 48 " pdb=" C2 C C 48 " ideal model delta sinusoidal sigma weight residual -160.00 -57.34 -102.66 1 1.50e+01 4.44e-03 5.20e+01 dihedral pdb=" O4' U X 20 " pdb=" C1' U X 20 " pdb=" N1 U X 20 " pdb=" C2 U X 20 " ideal model delta sinusoidal sigma weight residual -160.00 -78.93 -81.07 1 1.50e+01 4.44e-03 3.60e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1035 0.043 - 0.085: 195 0.085 - 0.128: 77 0.128 - 0.171: 98 0.171 - 0.213: 1 Chirality restraints: 1406 Sorted by residual: chirality pdb=" C1' U C 39 " pdb=" O4' U C 39 " pdb=" C2' U C 39 " pdb=" N1 U C 39 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C1' A X 58 " pdb=" O4' A X 58 " pdb=" C2' A X 58 " pdb=" N9 A X 58 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 1403 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 267 " -0.010 2.00e-02 2.50e+03 1.50e-02 3.94e+00 pdb=" CG PHE A 267 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 267 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 267 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 267 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 267 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 295 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 296 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 124 " 0.007 2.00e-02 2.50e+03 1.04e-02 1.88e+00 pdb=" CG PHE A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 124 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 124 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 124 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 124 " -0.000 2.00e-02 2.50e+03 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 947 2.75 - 3.28: 7297 3.28 - 3.82: 13914 3.82 - 4.36: 16028 4.36 - 4.90: 24623 Nonbonded interactions: 62809 Sorted by model distance: nonbonded pdb=" O2' A C 7 " pdb=" O2 C C 48 " model vdw 2.207 3.040 nonbonded pdb=" O2' A X 7 " pdb=" O2 C X 48 " model vdw 2.255 3.040 nonbonded pdb=" O2' A C 57 " pdb=" OP2 U C 59 " model vdw 2.294 3.040 nonbonded pdb=" ND2 ASN B 224 " pdb=" O LEU B 302 " model vdw 2.296 3.120 nonbonded pdb=" O GLY A 115 " pdb=" NE2 GLN A 126 " model vdw 2.306 3.120 ... (remaining 62804 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'X' } 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=0.00 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.970 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 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 : 0.003 0.028 8206 Z= 0.207 Angle : 0.670 8.284 11766 Z= 0.503 Chirality : 0.052 0.213 1406 Planarity : 0.003 0.036 996 Dihedral : 21.865 164.067 3986 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.39 % Allowed : 35.94 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.35), residues: 570 helix: 1.83 (0.43), residues: 146 sheet: -0.83 (0.51), residues: 100 loop : -1.57 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 193 TYR 0.007 0.001 TYR A 160 PHE 0.034 0.002 PHE A 267 TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.21 ( 8206) covalent geometry : angle 0.66974 / 0.50 (11766) hydrogen bonds : bond 0.15875 / 10.68 ( 300) hydrogen bonds : angle 5.60649 / 3.93 ( 719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.231 Fit side-chains REVERT: A 119 LYS cc_start: 0.6643 (pttt) cc_final: 0.6378 (ptmm) REVERT: A 228 MET cc_start: 0.6839 (mtm) cc_final: 0.6537 (mtp) REVERT: A 313 GLN cc_start: 0.5796 (tp-100) cc_final: 0.5578 (mt0) REVERT: A 316 MET cc_start: 0.5871 (ptp) cc_final: 0.5106 (ptt) REVERT: A 320 PHE cc_start: 0.6789 (p90) cc_final: 0.5657 (p90) REVERT: A 328 LYS cc_start: 0.5720 (ttmm) cc_final: 0.5416 (ttpt) REVERT: A 331 ASN cc_start: 0.7059 (m-40) cc_final: 0.6816 (m-40) REVERT: B 210 ASP cc_start: 0.6151 (t0) cc_final: 0.5942 (t0) REVERT: B 247 GLN cc_start: 0.6086 (pt0) cc_final: 0.5368 (pm20) REVERT: B 347 HIS cc_start: 0.5805 (t70) cc_final: 0.5526 (t-170) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.1115 time to fit residues: 14.5126 Evaluate side-chains 65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN A 238 GLN A 247 GLN B 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.192431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157763 restraints weight = 8823.901| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.34 r_work: 0.3762 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8206 Z= 0.228 Angle : 0.649 9.368 11766 Z= 0.355 Chirality : 0.043 0.192 1406 Planarity : 0.005 0.042 996 Dihedral : 21.320 163.832 2821 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.69 % Allowed : 31.84 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.34), residues: 570 helix: 1.39 (0.41), residues: 146 sheet: -0.47 (0.50), residues: 90 loop : -1.65 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 280 TYR 0.016 0.002 TYR A 76 PHE 0.027 0.003 PHE A 320 TRP 0.008 0.002 TRP B 177 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 ( 8206) covalent geometry : angle 0.64858 / 0.35 (11766) hydrogen bonds : bond 0.07450 / 5.08 ( 300) hydrogen bonds : angle 4.76904 / 3.33 ( 719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8497 (pttt) cc_final: 0.8293 (ptmm) REVERT: A 316 MET cc_start: 0.6311 (ptp) cc_final: 0.6034 (ptt) REVERT: B 64 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6186 (t-90) REVERT: B 82 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: B 247 GLN cc_start: 0.6106 (pt0) cc_final: 0.5799 (pm20) REVERT: B 303 LEU cc_start: 0.7372 (pp) cc_final: 0.6560 (mt) outliers start: 24 outliers final: 14 residues processed: 75 average time/residue: 0.0757 time to fit residues: 7.9497 Evaluate side-chains 68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.0060 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.198648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.164866 restraints weight = 8781.997| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.33 r_work: 0.3846 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3700 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8206 Z= 0.109 Angle : 0.482 8.349 11766 Z= 0.275 Chirality : 0.035 0.203 1406 Planarity : 0.004 0.032 996 Dihedral : 21.090 159.818 2821 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.93 % Allowed : 32.42 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.35), residues: 570 helix: 1.60 (0.42), residues: 146 sheet: -0.26 (0.51), residues: 90 loop : -1.42 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.006 0.001 TYR A 216 PHE 0.018 0.001 PHE A 320 TRP 0.005 0.001 TRP B 352 HIS 0.017 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 ( 8206) covalent geometry : angle 0.48189 / 0.28 (11766) hydrogen bonds : bond 0.05761 / 3.86 ( 300) hydrogen bonds : angle 4.34493 / 3.06 ( 719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.225 Fit side-chains REVERT: A 304 ASN cc_start: 0.6845 (m-40) cc_final: 0.5939 (t0) REVERT: A 316 MET cc_start: 0.5994 (ptp) cc_final: 0.5674 (ptt) REVERT: B 303 LEU cc_start: 0.7335 (pp) cc_final: 0.6622 (mt) outliers start: 15 outliers final: 7 residues processed: 68 average time/residue: 0.0692 time to fit residues: 6.8964 Evaluate side-chains 58 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 279 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 0.0010 chunk 47 optimal weight: 2.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.199766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166142 restraints weight = 8958.301| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.39 r_work: 0.3851 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8206 Z= 0.096 Angle : 0.451 8.051 11766 Z= 0.258 Chirality : 0.034 0.204 1406 Planarity : 0.003 0.031 996 Dihedral : 20.947 156.649 2818 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.93 % Allowed : 32.03 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.35), residues: 570 helix: 2.23 (0.42), residues: 134 sheet: -0.18 (0.51), residues: 90 loop : -1.35 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.007 0.001 TYR A 160 PHE 0.020 0.001 PHE A 320 TRP 0.005 0.001 TRP A 352 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 ( 8206) covalent geometry : angle 0.45083 / 0.26 (11766) hydrogen bonds : bond 0.05272 / 3.54 ( 300) hydrogen bonds : angle 4.17527 / 2.95 ( 719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.199 Fit side-chains REVERT: A 131 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6658 (t0) REVERT: A 304 ASN cc_start: 0.6782 (m-40) cc_final: 0.5967 (t0) REVERT: A 316 MET cc_start: 0.5907 (ptp) cc_final: 0.5679 (ptt) REVERT: B 260 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6510 (tp30) REVERT: B 303 LEU cc_start: 0.7449 (pp) cc_final: 0.6830 (mt) outliers start: 15 outliers final: 8 residues processed: 72 average time/residue: 0.0751 time to fit residues: 7.6685 Evaluate side-chains 62 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.196906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162031 restraints weight = 8744.889| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.38 r_work: 0.3824 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8206 Z= 0.104 Angle : 0.452 7.898 11766 Z= 0.257 Chirality : 0.034 0.207 1406 Planarity : 0.003 0.031 996 Dihedral : 20.899 154.514 2818 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.49 % Allowed : 29.88 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.35), residues: 570 helix: 2.38 (0.43), residues: 134 sheet: -0.11 (0.50), residues: 90 loop : -1.34 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.007 0.001 TYR A 195 PHE 0.023 0.001 PHE A 320 TRP 0.006 0.001 TRP A 352 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 8206) covalent geometry : angle 0.45213 / 0.26 (11766) hydrogen bonds : bond 0.05295 / 3.57 ( 300) hydrogen bonds : angle 4.11531 / 2.90 ( 719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.229 Fit side-chains REVERT: A 131 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6686 (t0) REVERT: A 275 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 304 ASN cc_start: 0.6739 (m-40) cc_final: 0.5946 (t0) REVERT: A 316 MET cc_start: 0.6064 (ptp) cc_final: 0.5846 (ptt) REVERT: B 82 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: B 260 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6426 (tp30) REVERT: B 303 LEU cc_start: 0.7388 (pp) cc_final: 0.6830 (mt) outliers start: 23 outliers final: 16 residues processed: 69 average time/residue: 0.0681 time to fit residues: 7.0032 Evaluate side-chains 69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.191597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.156981 restraints weight = 8798.037| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.31 r_work: 0.3762 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8206 Z= 0.179 Angle : 0.554 8.331 11766 Z= 0.305 Chirality : 0.039 0.207 1406 Planarity : 0.004 0.039 996 Dihedral : 20.979 153.823 2818 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.47 % Allowed : 28.71 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.35), residues: 570 helix: 1.67 (0.42), residues: 146 sheet: -0.33 (0.50), residues: 90 loop : -1.43 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 280 TYR 0.014 0.002 TYR A 195 PHE 0.029 0.002 PHE A 320 TRP 0.007 0.001 TRP A 352 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 ( 8206) covalent geometry : angle 0.55430 / 0.31 (11766) hydrogen bonds : bond 0.06376 / 4.36 ( 300) hydrogen bonds : angle 4.23704 / 2.96 ( 719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: A 131 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6782 (t0) REVERT: A 304 ASN cc_start: 0.6813 (m-40) cc_final: 0.6114 (t0) REVERT: A 316 MET cc_start: 0.6617 (ptp) cc_final: 0.6375 (ptt) REVERT: B 82 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7281 (mt0) REVERT: B 260 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6588 (tp30) REVERT: B 279 VAL cc_start: 0.6868 (OUTLIER) cc_final: 0.6654 (m) REVERT: B 303 LEU cc_start: 0.7384 (pp) cc_final: 0.6660 (mt) REVERT: B 350 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6309 (mt0) outliers start: 28 outliers final: 16 residues processed: 73 average time/residue: 0.0596 time to fit residues: 6.5830 Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.192184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.157418 restraints weight = 8766.788| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.33 r_work: 0.3761 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8206 Z= 0.157 Angle : 0.532 8.628 11766 Z= 0.294 Chirality : 0.037 0.212 1406 Planarity : 0.004 0.036 996 Dihedral : 20.944 152.854 2818 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.66 % Allowed : 27.93 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.35), residues: 570 helix: 1.46 (0.43), residues: 146 sheet: -0.30 (0.50), residues: 90 loop : -1.45 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.011 0.001 TYR A 195 PHE 0.026 0.002 PHE A 320 TRP 0.006 0.001 TRP A 177 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 8206) covalent geometry : angle 0.53249 / 0.29 (11766) hydrogen bonds : bond 0.06203 / 4.23 ( 300) hydrogen bonds : angle 4.23160 / 2.96 ( 719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 52 time to evaluate : 0.187 Fit side-chains REVERT: A 77 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: A 131 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6820 (t0) REVERT: A 304 ASN cc_start: 0.6714 (m-40) cc_final: 0.6052 (t0) REVERT: A 316 MET cc_start: 0.6683 (ptp) cc_final: 0.6437 (ptt) REVERT: B 82 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7346 (mt0) REVERT: B 279 VAL cc_start: 0.6855 (OUTLIER) cc_final: 0.6631 (m) REVERT: B 303 LEU cc_start: 0.7358 (pp) cc_final: 0.6582 (mt) REVERT: B 304 ASN cc_start: 0.7003 (m-40) cc_final: 0.6723 (m-40) REVERT: B 350 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6279 (mt0) outliers start: 29 outliers final: 19 residues processed: 73 average time/residue: 0.0652 time to fit residues: 7.0295 Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 50.0000 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.192711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.157549 restraints weight = 8849.631| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.40 r_work: 0.3770 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8206 Z= 0.137 Angle : 0.512 8.359 11766 Z= 0.285 Chirality : 0.036 0.210 1406 Planarity : 0.004 0.035 996 Dihedral : 20.902 152.337 2818 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.27 % Allowed : 28.32 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.35), residues: 570 helix: 1.41 (0.43), residues: 146 sheet: -0.25 (0.50), residues: 90 loop : -1.45 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.010 0.001 TYR A 195 PHE 0.025 0.002 PHE A 320 TRP 0.005 0.001 TRP A 352 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8206) covalent geometry : angle 0.51151 / 0.29 (11766) hydrogen bonds : bond 0.05969 / 4.06 ( 300) hydrogen bonds : angle 4.20537 / 2.94 ( 719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 49 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6490 (mp10) REVERT: A 131 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6778 (t0) REVERT: A 304 ASN cc_start: 0.6647 (m-40) cc_final: 0.6036 (t0) REVERT: A 316 MET cc_start: 0.6645 (ptp) cc_final: 0.6416 (ptt) REVERT: B 82 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: B 279 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6626 (m) REVERT: B 303 LEU cc_start: 0.7380 (pp) cc_final: 0.6571 (mt) REVERT: B 304 ASN cc_start: 0.7003 (m-40) cc_final: 0.6676 (m-40) REVERT: B 350 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6290 (mt0) outliers start: 27 outliers final: 19 residues processed: 70 average time/residue: 0.0611 time to fit residues: 6.3710 Evaluate side-chains 73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 220 HIS Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.195226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.160022 restraints weight = 8851.219| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.44 r_work: 0.3817 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8206 Z= 0.106 Angle : 0.471 8.921 11766 Z= 0.265 Chirality : 0.034 0.207 1406 Planarity : 0.003 0.032 996 Dihedral : 20.808 151.139 2818 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 29.30 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.35), residues: 570 helix: 1.51 (0.44), residues: 146 sheet: -0.18 (0.51), residues: 90 loop : -1.42 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 280 TYR 0.007 0.001 TYR A 314 PHE 0.022 0.001 PHE A 320 TRP 0.005 0.001 TRP A 352 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 ( 8206) covalent geometry : angle 0.47119 / 0.26 (11766) hydrogen bonds : bond 0.05347 / 3.62 ( 300) hydrogen bonds : angle 4.07238 / 2.85 ( 719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.250 Fit side-chains REVERT: A 77 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6386 (mp10) REVERT: A 131 ASP cc_start: 0.6974 (OUTLIER) cc_final: 0.6705 (t0) REVERT: A 304 ASN cc_start: 0.6524 (m-40) cc_final: 0.5777 (t0) REVERT: A 316 MET cc_start: 0.6621 (ptp) cc_final: 0.6364 (ptt) REVERT: B 82 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: B 92 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7917 (mmtt) REVERT: B 303 LEU cc_start: 0.7300 (pp) cc_final: 0.6533 (mt) REVERT: B 304 ASN cc_start: 0.6863 (m-40) cc_final: 0.6586 (m-40) REVERT: B 350 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6287 (mt0) outliers start: 23 outliers final: 13 residues processed: 69 average time/residue: 0.0732 time to fit residues: 7.2641 Evaluate side-chains 68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 30.0000 chunk 63 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.190521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.155314 restraints weight = 8787.813| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.36 r_work: 0.3750 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8206 Z= 0.184 Angle : 0.575 8.934 11766 Z= 0.313 Chirality : 0.039 0.199 1406 Planarity : 0.005 0.037 996 Dihedral : 20.916 151.579 2818 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.30 % Allowed : 28.71 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.35), residues: 570 helix: 1.26 (0.43), residues: 146 sheet: -0.37 (0.51), residues: 90 loop : -1.52 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 280 TYR 0.013 0.002 TYR A 195 PHE 0.029 0.002 PHE A 320 TRP 0.008 0.002 TRP A 352 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 8206) covalent geometry : angle 0.57473 / 0.31 (11766) hydrogen bonds : bond 0.06487 / 4.43 ( 300) hydrogen bonds : angle 4.25064 / 2.96 ( 719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: A 131 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6861 (t0) REVERT: A 238 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.6358 (tm130) REVERT: A 304 ASN cc_start: 0.6580 (m-40) cc_final: 0.5926 (t0) REVERT: A 316 MET cc_start: 0.6766 (ptp) cc_final: 0.6514 (ptt) REVERT: B 82 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: B 92 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7961 (mmtt) REVERT: B 303 LEU cc_start: 0.7382 (pp) cc_final: 0.6472 (mt) REVERT: B 304 ASN cc_start: 0.7007 (m-40) cc_final: 0.6702 (m-40) REVERT: B 350 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6287 (mt0) outliers start: 22 outliers final: 14 residues processed: 67 average time/residue: 0.0786 time to fit residues: 7.5934 Evaluate side-chains 65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.191869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.157067 restraints weight = 8872.116| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.41 r_work: 0.3782 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8206 Z= 0.152 Angle : 0.531 9.466 11766 Z= 0.294 Chirality : 0.037 0.199 1406 Planarity : 0.004 0.034 996 Dihedral : 20.888 151.151 2818 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.91 % Allowed : 29.10 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.35), residues: 570 helix: 0.99 (0.43), residues: 158 sheet: -0.36 (0.50), residues: 90 loop : -1.50 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 280 TYR 0.011 0.001 TYR A 195 PHE 0.033 0.002 PHE A 79 TRP 0.006 0.001 TRP A 352 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8206) covalent geometry : angle 0.53144 / 0.29 (11766) hydrogen bonds : bond 0.06095 / 4.15 ( 300) hydrogen bonds : angle 4.22889 / 2.95 ( 719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.92 seconds wall clock time: 35 minutes 56.19 seconds (2156.19 seconds total)