Starting phenix.real_space_refine on Thu Jul 2 07:29:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8okd_16926/07_2026/8okd_16926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8okd_16926/07_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_16926/07_2026/8okd_16926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8okd_16926/07_2026/8okd_16926.map" model { file = "/net/cci-nas-00/data/ceres_data/8okd_16926/07_2026/8okd_16926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8okd_16926/07_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-dev-6108/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: 1.68, per 1000 atoms: 0.22 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: 0.53 Conformation dependent library (CDL) restraints added in 326.7 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: 1.06 Time building geometry restraints manager: 0.73 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: 11572 1.66 - 3.31: 167 3.31 - 4.97: 21 4.97 - 6.63: 3 6.63 - 8.28: 3 Bond angle restraints: 11766 Sorted by residual: angle pdb=" N GLY A 233 " pdb=" CA GLY A 233 " pdb=" C GLY A 233 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.10e+01 angle pdb=" C1' C C 41 " pdb=" N1 C C 41 " pdb=" C2 C C 41 " ideal model delta sigma weight residual 118.80 122.18 -3.38 1.10e+00 8.26e-01 9.45e+00 angle pdb=" C1' U C 39 " pdb=" N1 U C 39 " pdb=" C2 U C 39 " ideal model delta sigma weight residual 117.70 114.04 3.66 1.20e+00 6.94e-01 9.29e+00 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 120.98 -8.28 3.00e+00 1.11e-01 7.63e+00 angle pdb=" N1 U X 26 " pdb=" C2 U X 26 " pdb=" O2 U X 26 " ideal model delta sigma weight residual 122.80 124.73 -1.93 7.00e-01 2.04e+00 7.60e+00 ... (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 - 0.042: 1177 0.042 - 0.083: 169 0.083 - 0.125: 54 0.125 - 0.167: 5 0.167 - 0.208: 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 1.08e+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=" CA PHE A 320 " pdb=" N PHE A 320 " pdb=" C PHE A 320 " pdb=" CB PHE A 320 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.930 Find NCS groups from input model: 0.090 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- 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= 0.191 Angle : 0.509 8.284 11766 Z= 0.364 Chirality : 0.034 0.208 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 0.00285 / 0.19 ( 8206) covalent geometry : angle 0.50940 / 0.36 (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 : 0.140 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: 0.0847 time to fit residues: 11.0334 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 : 0.128 ------------------------------------------------------------------------------- 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: 20.0000 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 238 GLN A 247 GLN B 64 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.192038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157569 restraints weight = 8829.307| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.32 r_work: 0.3759 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8206 Z= 0.233 Angle : 0.648 9.551 11766 Z= 0.358 Chirality : 0.043 0.312 1406 Planarity : 0.005 0.044 996 Dihedral : 21.362 166.649 2821 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.27 % Allowed : 30.47 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.95 (0.34), residues: 570 helix: 1.29 (0.41), residues: 146 sheet: -0.47 (0.50), residues: 90 loop : -1.64 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 280 TYR 0.018 0.002 TYR A 76 PHE 0.027 0.003 PHE A 320 TRP 0.009 0.002 TRP B 177 HIS 0.005 0.002 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 ( 8206) covalent geometry : angle 0.64772 / 0.36 (11766) hydrogen bonds : bond 0.07174 / 4.94 ( 300) hydrogen bonds : angle 4.73747 / 3.31 ( 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 86 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 119 LYS cc_start: 0.8506 (pttt) cc_final: 0.8165 (ptmm) REVERT: A 131 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 316 MET cc_start: 0.6372 (ptp) cc_final: 0.6052 (ptt) REVERT: B 64 HIS cc_start: 0.6824 (OUTLIER) cc_final: 0.6234 (t-90) REVERT: B 82 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7171 (mt0) REVERT: B 247 GLN cc_start: 0.6137 (pt0) cc_final: 0.5805 (pm20) REVERT: B 303 LEU cc_start: 0.7363 (pp) cc_final: 0.6532 (mt) outliers start: 27 outliers final: 13 residues processed: 77 average time/residue: 0.0762 time to fit residues: 8.1748 Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.197162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.163607 restraints weight = 8736.875| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.28 r_work: 0.3845 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8206 Z= 0.106 Angle : 0.473 8.279 11766 Z= 0.272 Chirality : 0.035 0.193 1406 Planarity : 0.004 0.034 996 Dihedral : 21.172 162.877 2821 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.93 % Allowed : 32.81 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.35), residues: 570 helix: 1.52 (0.42), residues: 146 sheet: -0.31 (0.51), residues: 90 loop : -1.43 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 193 TYR 0.007 0.001 TYR A 160 PHE 0.018 0.001 PHE A 320 TRP 0.005 0.001 TRP A 352 HIS 0.013 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 8206) covalent geometry : angle 0.47331 / 0.27 (11766) hydrogen bonds : bond 0.05518 / 3.72 ( 300) hydrogen bonds : angle 4.37585 / 3.07 ( 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 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.207 Fit side-chains REVERT: A 304 ASN cc_start: 0.6831 (m-40) cc_final: 0.5962 (t0) REVERT: A 316 MET cc_start: 0.6115 (ptp) cc_final: 0.5823 (ptt) REVERT: B 303 LEU cc_start: 0.7346 (pp) cc_final: 0.6618 (mt) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.0654 time to fit residues: 6.1498 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 : 0.160 ------------------------------------------------------------------------------- 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 A residue 320 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.196830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.162398 restraints weight = 8929.024| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.34 r_work: 0.3817 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8206 Z= 0.109 Angle : 0.458 8.250 11766 Z= 0.263 Chirality : 0.035 0.218 1406 Planarity : 0.004 0.035 996 Dihedral : 21.043 161.200 2818 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.10 % Allowed : 31.05 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.56 (0.35), residues: 570 helix: 1.67 (0.42), residues: 146 sheet: -0.27 (0.51), residues: 90 loop : -1.40 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.007 0.001 TYR A 195 PHE 0.022 0.001 PHE A 320 TRP 0.006 0.001 TRP A 352 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 8206) covalent geometry : angle 0.45779 / 0.26 (11766) hydrogen bonds : bond 0.05284 / 3.60 ( 300) hydrogen bonds : angle 4.20175 / 2.96 ( 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 76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.182 Fit side-chains REVERT: A 275 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7589 (tt) REVERT: A 304 ASN cc_start: 0.6844 (m-40) cc_final: 0.5990 (t0) REVERT: A 316 MET cc_start: 0.6091 (ptp) cc_final: 0.5819 (ptt) REVERT: B 82 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: B 303 LEU cc_start: 0.7332 (pp) cc_final: 0.6592 (mt) REVERT: B 350 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6281 (mt0) outliers start: 21 outliers final: 13 residues processed: 70 average time/residue: 0.0556 time to fit residues: 5.8144 Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 369 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 318 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 47 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.198679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164869 restraints weight = 8813.967| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.38 r_work: 0.3840 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8206 Z= 0.096 Angle : 0.442 7.818 11766 Z= 0.254 Chirality : 0.034 0.191 1406 Planarity : 0.003 0.032 996 Dihedral : 20.977 158.933 2818 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.69 % Allowed : 29.30 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.35), residues: 570 helix: 2.29 (0.42), residues: 134 sheet: -0.07 (0.51), residues: 90 loop : -1.33 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 280 TYR 0.006 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 0.00193 / 0.10 ( 8206) covalent geometry : angle 0.44247 / 0.25 (11766) hydrogen bonds : bond 0.04955 / 3.36 ( 300) hydrogen bonds : angle 4.11732 / 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 77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6248 (mp10) REVERT: A 247 GLN cc_start: 0.5688 (mt0) cc_final: 0.5314 (mt0) REVERT: A 275 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7605 (tt) REVERT: A 304 ASN cc_start: 0.6685 (m-40) cc_final: 0.5877 (t0) REVERT: A 316 MET cc_start: 0.6107 (ptp) cc_final: 0.5847 (ptt) REVERT: B 303 LEU cc_start: 0.7409 (pp) cc_final: 0.6855 (mt) REVERT: B 350 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6270 (mt0) outliers start: 24 outliers final: 14 residues processed: 70 average time/residue: 0.0671 time to fit residues: 6.8469 Evaluate side-chains 64 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 311 LYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 369 LEU 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 318 VAL Chi-restraints excluded: chain B residue 350 GLN 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: 6.9990 chunk 4 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.194254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159799 restraints weight = 8765.653| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.37 r_work: 0.3808 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8206 Z= 0.120 Angle : 0.466 7.952 11766 Z= 0.265 Chirality : 0.036 0.225 1406 Planarity : 0.004 0.036 996 Dihedral : 20.948 157.230 2818 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.08 % Allowed : 28.32 % Favored : 66.60 % 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: 2.32 (0.43), residues: 134 sheet: -0.20 (0.51), residues: 90 loop : -1.38 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.010 0.001 TYR A 71 PHE 0.025 0.002 PHE A 320 TRP 0.007 0.001 TRP A 352 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8206) covalent geometry : angle 0.46609 / 0.26 (11766) hydrogen bonds : bond 0.05363 / 3.65 ( 300) hydrogen bonds : angle 4.06772 / 2.85 ( 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 77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.268 Fit side-chains REVERT: A 77 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6366 (mp10) REVERT: A 275 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 304 ASN cc_start: 0.6679 (m-40) cc_final: 0.5990 (t0) REVERT: A 316 MET cc_start: 0.6443 (ptp) cc_final: 0.6240 (ptt) REVERT: B 82 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7249 (mp10) REVERT: B 303 LEU cc_start: 0.7355 (pp) cc_final: 0.6826 (mt) REVERT: B 350 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6231 (mt0) outliers start: 26 outliers final: 14 residues processed: 69 average time/residue: 0.0653 time to fit residues: 6.6708 Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain A residue 238 GLN Chi-restraints excluded: chain A residue 275 LEU 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 359 THR 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 266 GLN Chi-restraints excluded: chain B residue 318 VAL 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: 0.8980 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.194522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.159974 restraints weight = 8788.431| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.33 r_work: 0.3795 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8206 Z= 0.140 Angle : 0.490 8.399 11766 Z= 0.277 Chirality : 0.037 0.232 1406 Planarity : 0.004 0.037 996 Dihedral : 20.950 156.332 2818 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.69 % Allowed : 28.52 % Favored : 66.80 % 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: -0.50 (0.35), residues: 570 helix: 2.12 (0.43), residues: 134 sheet: -0.26 (0.50), residues: 90 loop : -1.44 (0.33), residues: 346 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 0.025 0.002 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 0.00313 / 0.14 ( 8206) covalent geometry : angle 0.49045 / 0.28 (11766) hydrogen bonds : bond 0.05545 / 3.81 ( 300) hydrogen bonds : angle 4.10147 / 2.87 ( 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 72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.197 Fit side-chains REVERT: A 77 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6404 (mp10) REVERT: A 304 ASN cc_start: 0.6633 (m-40) cc_final: 0.5990 (t0) REVERT: A 316 MET cc_start: 0.6518 (ptp) cc_final: 0.6308 (ptt) REVERT: B 82 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: B 303 LEU cc_start: 0.7357 (pp) cc_final: 0.6782 (mt) REVERT: B 304 ASN cc_start: 0.7074 (m-40) cc_final: 0.6781 (m-40) REVERT: B 350 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6266 (mt0) outliers start: 24 outliers final: 17 residues processed: 66 average time/residue: 0.0611 time to fit residues: 6.1165 Evaluate side-chains 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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 234 VAL 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 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: 20.0000 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 50.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 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 = 0.4360 r_free = 0.4360 target = 0.192510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.157602 restraints weight = 8833.031| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.32 r_work: 0.3766 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8206 Z= 0.147 Angle : 0.496 8.237 11766 Z= 0.280 Chirality : 0.037 0.241 1406 Planarity : 0.004 0.035 996 Dihedral : 20.939 156.040 2818 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.49 % Allowed : 28.32 % Favored : 67.19 % 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: 1.95 (0.44), residues: 134 sheet: -0.29 (0.51), residues: 90 loop : -1.45 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 280 TYR 0.011 0.001 TYR A 195 PHE 0.025 0.002 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 0.00332 / 0.15 ( 8206) covalent geometry : angle 0.49621 / 0.28 (11766) hydrogen bonds : bond 0.05693 / 3.89 ( 300) hydrogen bonds : angle 4.15511 / 2.90 ( 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: 23 poor density : 53 time to evaluate : 0.169 Fit side-chains REVERT: A 77 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.6485 (mp10) REVERT: A 304 ASN cc_start: 0.6640 (m-40) cc_final: 0.5954 (t0) REVERT: B 82 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: B 92 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7880 (mmtt) REVERT: B 303 LEU cc_start: 0.7367 (pp) cc_final: 0.6720 (mt) REVERT: B 304 ASN cc_start: 0.7055 (m-40) cc_final: 0.6734 (m-40) REVERT: B 350 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6274 (mt0) outliers start: 23 outliers final: 18 residues processed: 71 average time/residue: 0.0566 time to fit residues: 5.9536 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 : 0.188 ------------------------------------------------------------------------------- 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 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 92 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 220 HIS 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 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: 10.0000 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 0.0470 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.195772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.160883 restraints weight = 8773.734| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.38 r_work: 0.3807 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2655 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= 0.105 Angle : 0.453 7.818 11766 Z= 0.258 Chirality : 0.035 0.205 1406 Planarity : 0.003 0.031 996 Dihedral : 20.868 154.934 2818 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.52 % Allowed : 29.30 % Favored : 67.19 % 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: -0.45 (0.35), residues: 570 helix: 1.68 (0.44), residues: 146 sheet: -0.10 (0.51), residues: 90 loop : -1.33 (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 160 PHE 0.033 0.002 PHE A 79 TRP 0.004 0.001 TRP A 352 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 8206) covalent geometry : angle 0.45268 / 0.26 (11766) hydrogen bonds : bond 0.05022 / 3.42 ( 300) hydrogen bonds : angle 4.05976 / 2.84 ( 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 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6353 (mp10) REVERT: A 304 ASN cc_start: 0.6612 (m-40) cc_final: 0.5844 (t0) REVERT: B 82 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: B 92 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7869 (mmtt) REVERT: B 303 LEU cc_start: 0.7348 (pp) cc_final: 0.6666 (mt) REVERT: B 304 ASN cc_start: 0.6982 (m-40) cc_final: 0.6652 (m-40) REVERT: B 350 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6306 (mt0) outliers start: 18 outliers final: 11 residues processed: 65 average time/residue: 0.0642 time to fit residues: 5.9710 Evaluate side-chains 63 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN 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 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: 0.8980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.191797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.157068 restraints weight = 8740.596| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.31 r_work: 0.3752 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8206 Z= 0.161 Angle : 0.515 8.247 11766 Z= 0.289 Chirality : 0.038 0.255 1406 Planarity : 0.004 0.036 996 Dihedral : 20.917 155.364 2818 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.71 % Allowed : 28.52 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.35), residues: 570 helix: 1.54 (0.43), residues: 146 sheet: -0.33 (0.51), residues: 90 loop : -1.41 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 280 TYR 0.012 0.002 TYR A 71 PHE 0.028 0.002 PHE A 320 TRP 0.007 0.001 TRP A 352 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8206) covalent geometry : angle 0.51530 / 0.29 (11766) hydrogen bonds : bond 0.05912 / 4.04 ( 300) hydrogen bonds : angle 4.14533 / 2.90 ( 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 67 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.160 Fit side-chains REVERT: A 77 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6483 (mp10) REVERT: A 238 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6357 (tm130) REVERT: B 82 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: B 92 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7909 (mmtt) REVERT: B 303 LEU cc_start: 0.7378 (pp) cc_final: 0.6587 (mt) REVERT: B 304 ASN cc_start: 0.7127 (m-40) cc_final: 0.6788 (m-40) REVERT: B 350 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6293 (mt0) outliers start: 19 outliers final: 13 residues processed: 64 average time/residue: 0.0682 time to fit residues: 6.3066 Evaluate side-chains 65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 161 THR Chi-restraints excluded: chain B residue 220 HIS 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 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: 20.0000 chunk 59 optimal weight: 9.9990 chunk 71 optimal weight: 40.0000 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 35 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 347 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.196479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160951 restraints weight = 8931.999| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.51 r_work: 0.3800 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2819 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 : 0.464 8.027 11766 Z= 0.263 Chirality : 0.035 0.211 1406 Planarity : 0.003 0.031 996 Dihedral : 20.864 154.434 2818 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.52 % Allowed : 28.71 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.36), residues: 570 helix: 1.62 (0.44), residues: 146 sheet: -0.17 (0.51), residues: 90 loop : -1.31 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 280 TYR 0.008 0.001 TYR A 314 PHE 0.038 0.002 PHE A 79 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 0.00225 / 0.11 ( 8206) covalent geometry : angle 0.46401 / 0.26 (11766) hydrogen bonds : bond 0.05125 / 3.49 ( 300) hydrogen bonds : angle 4.07420 / 2.84 ( 719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.48 seconds wall clock time: 32 minutes 23.63 seconds (1943.63 seconds total)