Starting phenix.real_space_refine on Fri Sep 11 00:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d9k_27264/09_2026/8d9k_27264.map" } resolution = 3.72 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= 0.006 sd= 0.030 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 65 5.49 5 S 21 5.16 5 C 3387 2.51 5 N 993 2.21 5 O 1242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1740 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 15, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2578 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 321} Chain breaks: 3 Chain: "C" Number of atoms: 1390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1390 Classifications: {'RNAv2': 65} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 29} Link IDs: {'rna2p': 8, 'rna3p': 56} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" N TYR A 37 " occ=0.88 ... (10 atoms not shown) pdb=" OH TYR A 37 " occ=0.88 residue: pdb=" N GLU A 43 " occ=0.83 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.83 residue: pdb=" N ASP A 45 " occ=0.96 ... (6 atoms not shown) pdb=" OD2 ASP A 45 " occ=0.96 residue: pdb=" N TYR A 50 " occ=0.90 ... (10 atoms not shown) pdb=" OH TYR A 50 " occ=0.90 residue: pdb=" N GLU A 52 " occ=0.87 ... (7 atoms not shown) pdb=" OE2 GLU A 52 " occ=0.87 residue: pdb=" N PHE A 53 " occ=0.93 ... (9 atoms not shown) pdb=" CZ PHE A 53 " occ=0.93 residue: pdb=" N PHE A 54 " occ=0.88 ... (9 atoms not shown) pdb=" CZ PHE A 54 " occ=0.88 residue: pdb=" N GLU A 79 " occ=0.85 ... (7 atoms not shown) pdb=" OE2 GLU A 79 " occ=0.85 residue: pdb=" N LYS A 111 " occ=0.98 ... (7 atoms not shown) pdb=" NZ LYS A 111 " occ=0.98 residue: pdb=" N ARG A 121 " occ=0.88 ... (9 atoms not shown) pdb=" NH2 ARG A 121 " occ=0.88 residue: pdb=" N ARG A 138 " occ=0.99 ... (9 atoms not shown) pdb=" NH2 ARG A 138 " occ=0.99 residue: pdb=" N MET A 142 " occ=0.86 ... (6 atoms not shown) pdb=" CE MET A 142 " occ=0.86 ... (remaining 31 not shown) Time building chain proxies: 1.24, per 1000 atoms: 0.22 Number of scatterers: 5708 At special positions: 0 Unit cell: (64.74, 100.845, 110.805, 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 21 16.00 P 65 15.00 O 1242 8.00 N 993 7.00 C 3387 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: 0.49 Conformation dependent library (CDL) restraints added in 298.4 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 8 sheets defined 22.7% alpha, 31.9% beta 27 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.844A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.629A pdb=" N ALA A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 221 through 226 removed outlier: 4.069A pdb=" N SER A 226 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.728A pdb=" N HIS A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.604A pdb=" N GLN B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 343 through 348 removed outlier: 4.398A pdb=" N LEU B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.975A pdb=" N SER B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 138 removed outlier: 5.498A pdb=" N VAL A 78 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU A 104 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 80 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N LEU A 106 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP A 82 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU A 79 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N MET A 157 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 81 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE A 159 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 83 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 192 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 69 removed outlier: 6.463A pdb=" N LEU B 85 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 98 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 87 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.655A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 126 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.951A pdb=" N ASP B 150 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 169 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP B 173 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 180 " --> pdb=" O TRP B 173 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.854A pdb=" N ARG B 193 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 213 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N CYS B 226 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 215 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.836A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLN B 272 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B 282 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP B 274 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU B 280 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 298 removed outlier: 3.981A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) 155 hydrogen bonds defined for protein. 426 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 0.95 Time building geometry restraints manager: 0.66 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: 1574 1.34 - 1.45: 1394 1.45 - 1.57: 2850 1.57 - 1.69: 128 1.69 - 1.81: 27 Bond restraints: 5973 Sorted by residual: bond pdb=" CG PRO B 92 " pdb=" CD PRO B 92 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.36e-01 bond pdb=" C1' G C 18 " pdb=" N9 G C 18 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 5.23e-01 bond pdb=" C1' A C 58 " pdb=" N9 A C 58 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 5.13e-01 bond pdb=" C1' G C 19 " pdb=" N9 G C 19 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 4.94e-01 bond pdb=" C1' G C 46 " pdb=" N9 G C 46 " ideal model delta sigma weight residual 1.478 1.464 0.014 2.00e-02 2.50e+03 4.70e-01 ... (remaining 5968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 8040 1.01 - 2.02: 157 2.02 - 3.03: 169 3.03 - 4.04: 23 4.04 - 5.06: 19 Bond angle restraints: 8408 Sorted by residual: angle pdb=" C TYR B 361 " pdb=" N LYS B 362 " pdb=" CA LYS B 362 " ideal model delta sigma weight residual 121.70 126.76 -5.06 1.80e+00 3.09e-01 7.89e+00 angle pdb=" C3' A C 9 " pdb=" C2' A C 9 " pdb=" O2' A C 9 " ideal model delta sigma weight residual 109.80 114.78 -4.98 2.00e+00 2.50e-01 6.20e+00 angle pdb=" C3' G C 19 " pdb=" C2' G C 19 " pdb=" O2' G C 19 " ideal model delta sigma weight residual 109.80 114.63 -4.83 2.00e+00 2.50e-01 5.84e+00 angle pdb=" C3' A C 58 " pdb=" C2' A C 58 " pdb=" O2' A C 58 " ideal model delta sigma weight residual 109.80 114.60 -4.80 2.00e+00 2.50e-01 5.76e+00 angle pdb=" C3' G C 46 " pdb=" C2' G C 46 " pdb=" O2' G C 46 " ideal model delta sigma weight residual 109.80 114.58 -4.78 2.00e+00 2.50e-01 5.72e+00 ... (remaining 8403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 3097 14.48 - 28.96: 145 28.96 - 43.43: 69 43.43 - 57.91: 53 57.91 - 72.39: 23 Dihedral angle restraints: 3387 sinusoidal: 1815 harmonic: 1572 Sorted by residual: dihedral pdb=" C4' A C 58 " pdb=" C3' A C 58 " pdb=" C2' A C 58 " pdb=" C1' A C 58 " ideal model delta sinusoidal sigma weight residual 36.35 -36.04 72.39 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' G C 46 " pdb=" C3' G C 46 " pdb=" C2' G C 46 " pdb=" C1' G C 46 " ideal model delta sinusoidal sigma weight residual 36.35 -35.60 71.95 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' G C 18 " pdb=" C3' G C 18 " pdb=" C2' G C 18 " pdb=" C1' G C 18 " ideal model delta sinusoidal sigma weight residual 36.35 -35.23 71.58 1 3.10e+00 1.04e-01 6.83e+02 ... (remaining 3384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 815 0.055 - 0.111: 83 0.111 - 0.166: 10 0.166 - 0.221: 2 0.221 - 0.277: 79 Chirality restraints: 989 Sorted by residual: chirality pdb=" C2' C C 48 " pdb=" C3' C C 48 " pdb=" O2' C C 48 " pdb=" C1' C C 48 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' G C 19 " pdb=" C3' G C 19 " pdb=" O2' G C 19 " pdb=" C1' G C 19 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C2' A C 7 " pdb=" C3' A C 7 " pdb=" O2' A C 7 " pdb=" C1' A C 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 986 not shown) Planarity restraints: 831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 59 " -0.013 2.00e-02 2.50e+03 6.11e-03 1.12e+00 pdb=" N9 G C 59 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C 59 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 59 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 59 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G C 59 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G C 59 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G C 59 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 59 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 59 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 228 " -0.016 5.00e-02 4.00e+02 2.39e-02 9.11e-01 pdb=" N PRO A 229 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 318 " -0.015 5.00e-02 4.00e+02 2.23e-02 7.97e-01 pdb=" N PRO B 319 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 319 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 319 " -0.012 5.00e-02 4.00e+02 ... (remaining 828 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1350 2.80 - 3.32: 5002 3.32 - 3.85: 10049 3.85 - 4.37: 11700 4.37 - 4.90: 18273 Nonbonded interactions: 46374 Sorted by model distance: nonbonded pdb=" ND1 HIS B 187 " pdb=" OG SER B 208 " model vdw 2.270 3.120 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 166 " model vdw 2.275 3.040 nonbonded pdb=" OP1 U C 60 " pdb=" N4 C C 61 " model vdw 2.296 3.120 nonbonded pdb=" O6 G C 10 " pdb=" N2 G C 45 " model vdw 2.303 3.120 nonbonded pdb=" OG1 THR B 188 " pdb=" OD2 ASP B 210 " model vdw 2.311 3.040 ... (remaining 46369 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.040 Find NCS groups from input model: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.002 0.020 5973 Z= 0.088 Angle : 0.577 5.055 8408 Z= 0.251 Chirality : 0.077 0.277 989 Planarity : 0.002 0.024 831 Dihedral : 13.498 72.387 2371 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.64 % Allowed : 5.77 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.53 (0.38), residues: 534 helix: 1.29 (0.58), residues: 103 sheet: 1.77 (0.39), residues: 185 loop : 0.37 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 318 TYR 0.004 0.001 TYR B 361 PHE 0.009 0.001 PHE A 166 TRP 0.006 0.001 TRP A 206 HIS 0.002 0.000 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.09 ( 5973) covalent geometry : angle 0.57722 / 0.25 ( 8408) hydrogen bonds : bond 0.14102 / 9.15 ( 224) hydrogen bonds : angle 4.94949 / 3.36 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9241 (t) cc_final: 0.8861 (p) REVERT: A 114 ASP cc_start: 0.9260 (t0) cc_final: 0.9017 (t0) REVERT: A 115 TYR cc_start: 0.9439 (t80) cc_final: 0.8910 (t80) REVERT: A 118 ASP cc_start: 0.9329 (m-30) cc_final: 0.9065 (m-30) REVERT: A 175 ILE cc_start: 0.9475 (mt) cc_final: 0.9114 (tp) REVERT: B 71 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8744 (tppt) REVERT: B 122 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8545 (ttpp) outliers start: 3 outliers final: 0 residues processed: 51 average time/residue: 0.0795 time to fit residues: 5.4028 Evaluate side-chains 20 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.033437 restraints weight = 34336.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.034515 restraints weight = 16790.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035226 restraints weight = 10971.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.035688 restraints weight = 8406.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.035982 restraints weight = 7097.817| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5973 Z= 0.307 Angle : 0.881 11.415 8408 Z= 0.381 Chirality : 0.062 0.490 989 Planarity : 0.003 0.021 831 Dihedral : 15.281 153.245 1364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 8.76 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.40 (0.38), residues: 534 helix: 1.90 (0.57), residues: 91 sheet: 1.58 (0.39), residues: 179 loop : 0.17 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 99 TYR 0.007 0.001 TYR A 150 PHE 0.010 0.002 PHE A 148 TRP 0.014 0.002 TRP A 206 HIS 0.010 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.31 ( 5973) covalent geometry : angle 0.88113 / 0.38 ( 8408) hydrogen bonds : bond 0.05505 / 3.19 ( 224) hydrogen bonds : angle 4.67481 / 3.13 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 TYR cc_start: 0.9582 (t80) cc_final: 0.9342 (t80) REVERT: A 175 ILE cc_start: 0.9588 (mt) cc_final: 0.9287 (tp) REVERT: B 71 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9123 (tppt) REVERT: B 87 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8632 (tt) outliers start: 8 outliers final: 2 residues processed: 28 average time/residue: 0.0836 time to fit residues: 3.1785 Evaluate side-chains 21 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 192 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.045153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.032449 restraints weight = 33044.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033495 restraints weight = 15665.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.034198 restraints weight = 10102.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.034628 restraints weight = 7622.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.034932 restraints weight = 6437.174| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5973 Z= 0.184 Angle : 0.669 9.669 8408 Z= 0.301 Chirality : 0.054 0.511 989 Planarity : 0.003 0.020 831 Dihedral : 15.143 161.562 1364 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.28 % Allowed : 10.47 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.21 (0.38), residues: 534 helix: 1.90 (0.57), residues: 97 sheet: 1.39 (0.39), residues: 179 loop : -0.00 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.005 0.001 TYR A 150 PHE 0.012 0.001 PHE A 166 TRP 0.009 0.001 TRP A 206 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 5973) covalent geometry : angle 0.66857 / 0.30 ( 8408) hydrogen bonds : bond 0.03961 / 2.50 ( 224) hydrogen bonds : angle 4.32259 / 2.90 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9264 (t) cc_final: 0.8934 (p) REVERT: A 115 TYR cc_start: 0.9550 (t80) cc_final: 0.9032 (t80) REVERT: A 175 ILE cc_start: 0.9586 (mt) cc_final: 0.9242 (tp) REVERT: B 71 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9179 (tppt) REVERT: B 87 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8714 (tt) outliers start: 6 outliers final: 1 residues processed: 25 average time/residue: 0.0769 time to fit residues: 2.6398 Evaluate side-chains 21 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.045780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.032797 restraints weight = 33574.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.033861 restraints weight = 16150.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034576 restraints weight = 10467.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.035004 restraints weight = 7941.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.035322 restraints weight = 6717.070| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5973 Z= 0.179 Angle : 0.652 8.135 8408 Z= 0.292 Chirality : 0.052 0.422 989 Planarity : 0.003 0.025 831 Dihedral : 15.024 168.599 1364 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.35 % Allowed : 9.40 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.08 (0.38), residues: 534 helix: 1.89 (0.57), residues: 97 sheet: 1.33 (0.39), residues: 178 loop : -0.16 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.006 0.001 TYR A 150 PHE 0.011 0.001 PHE A 166 TRP 0.013 0.001 TRP A 206 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 5973) covalent geometry : angle 0.65235 / 0.29 ( 8408) hydrogen bonds : bond 0.03848 / 2.38 ( 224) hydrogen bonds : angle 4.19976 / 2.80 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.192 Fit side-chains REVERT: A 95 SER cc_start: 0.9297 (t) cc_final: 0.8975 (p) REVERT: A 115 TYR cc_start: 0.9553 (t80) cc_final: 0.9070 (t80) REVERT: A 175 ILE cc_start: 0.9589 (mt) cc_final: 0.9237 (tp) REVERT: B 71 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9214 (tppt) REVERT: B 122 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8674 (ptpt) outliers start: 11 outliers final: 4 residues processed: 37 average time/residue: 0.0762 time to fit residues: 3.9158 Evaluate side-chains 23 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.046210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.033452 restraints weight = 33231.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034518 restraints weight = 16172.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.035224 restraints weight = 10439.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035695 restraints weight = 7886.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.035952 restraints weight = 6596.465| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5973 Z= 0.136 Angle : 0.626 9.124 8408 Z= 0.279 Chirality : 0.052 0.429 989 Planarity : 0.003 0.024 831 Dihedral : 14.917 169.852 1364 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.50 % Allowed : 10.47 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.08 (0.38), residues: 534 helix: 1.84 (0.57), residues: 97 sheet: 1.37 (0.39), residues: 172 loop : -0.11 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.004 0.001 TYR A 50 PHE 0.011 0.001 PHE A 166 TRP 0.007 0.001 TRP A 206 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 5973) covalent geometry : angle 0.62619 / 0.28 ( 8408) hydrogen bonds : bond 0.03335 / 2.12 ( 224) hydrogen bonds : angle 4.08524 / 2.74 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.187 Fit side-chains REVERT: A 95 SER cc_start: 0.9181 (t) cc_final: 0.8916 (p) REVERT: A 115 TYR cc_start: 0.9467 (t80) cc_final: 0.9235 (t80) REVERT: A 175 ILE cc_start: 0.9579 (mt) cc_final: 0.9270 (tp) REVERT: B 71 LYS cc_start: 0.9418 (tmtt) cc_final: 0.9192 (tppt) REVERT: B 122 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8767 (ptpt) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.0794 time to fit residues: 2.9422 Evaluate side-chains 24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.3111 r_free = 0.3111 target = 0.044784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.032010 restraints weight = 33682.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.033020 restraints weight = 16398.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.033716 restraints weight = 10773.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.034093 restraints weight = 8220.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.034418 restraints weight = 7063.549| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 5973 Z= 0.228 Angle : 0.704 7.888 8408 Z= 0.314 Chirality : 0.053 0.450 989 Planarity : 0.003 0.032 831 Dihedral : 15.027 169.877 1364 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 9.83 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.86 (0.38), residues: 534 helix: 1.68 (0.56), residues: 97 sheet: 1.18 (0.38), residues: 176 loop : -0.25 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 21 TYR 0.005 0.001 TYR A 50 PHE 0.010 0.001 PHE A 166 TRP 0.012 0.001 TRP A 206 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 ( 5973) covalent geometry : angle 0.70396 / 0.31 ( 8408) hydrogen bonds : bond 0.04148 / 2.63 ( 224) hydrogen bonds : angle 4.35933 / 2.93 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9336 (t) cc_final: 0.9049 (p) REVERT: A 115 TYR cc_start: 0.9569 (t80) cc_final: 0.9324 (t80) REVERT: A 175 ILE cc_start: 0.9585 (mt) cc_final: 0.9308 (tp) REVERT: B 71 LYS cc_start: 0.9467 (tmtt) cc_final: 0.9231 (tppt) REVERT: B 346 MET cc_start: 0.9201 (mmm) cc_final: 0.8968 (mmm) outliers start: 9 outliers final: 7 residues processed: 27 average time/residue: 0.0831 time to fit residues: 3.1229 Evaluate side-chains 25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.6104 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.046334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.033649 restraints weight = 33147.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.034703 restraints weight = 15869.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035419 restraints weight = 10212.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035862 restraints weight = 7695.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036164 restraints weight = 6459.950| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5973 Z= 0.109 Angle : 0.617 7.767 8408 Z= 0.273 Chirality : 0.052 0.411 989 Planarity : 0.003 0.028 831 Dihedral : 14.851 171.682 1364 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.50 % Allowed : 9.83 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.97 (0.38), residues: 534 helix: 1.77 (0.57), residues: 97 sheet: 1.23 (0.39), residues: 172 loop : -0.14 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.003 0.000 TYR B 269 PHE 0.011 0.001 PHE A 166 TRP 0.005 0.001 TRP B 173 HIS 0.004 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 5973) covalent geometry : angle 0.61749 / 0.27 ( 8408) hydrogen bonds : bond 0.03241 / 2.09 ( 224) hydrogen bonds : angle 4.01335 / 2.70 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9140 (t) cc_final: 0.8895 (p) REVERT: A 115 TYR cc_start: 0.9466 (t80) cc_final: 0.9258 (t80) REVERT: A 175 ILE cc_start: 0.9567 (mt) cc_final: 0.9240 (tp) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.0817 time to fit residues: 3.2153 Evaluate side-chains 24 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 335 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 4 optimal weight: 0.0030 chunk 8 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.046249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.033455 restraints weight = 32941.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.034519 restraints weight = 16191.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.035229 restraints weight = 10509.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035657 restraints weight = 7978.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.035894 restraints weight = 6747.687| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5973 Z= 0.123 Angle : 0.627 7.352 8408 Z= 0.282 Chirality : 0.052 0.417 989 Planarity : 0.003 0.027 831 Dihedral : 14.826 173.056 1364 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.28 % Allowed : 9.83 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.38), residues: 534 helix: 1.78 (0.57), residues: 97 sheet: 1.26 (0.39), residues: 170 loop : -0.19 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.014 0.001 TYR B 38 PHE 0.010 0.001 PHE A 166 TRP 0.012 0.001 TRP B 344 HIS 0.003 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 5973) covalent geometry : angle 0.62720 / 0.28 ( 8408) hydrogen bonds : bond 0.03390 / 2.20 ( 224) hydrogen bonds : angle 4.01093 / 2.70 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 SER cc_start: 0.9196 (t) cc_final: 0.8921 (p) REVERT: A 115 TYR cc_start: 0.9503 (t80) cc_final: 0.9293 (t80) REVERT: A 175 ILE cc_start: 0.9580 (mt) cc_final: 0.9248 (tp) REVERT: B 122 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8779 (ptpt) outliers start: 6 outliers final: 5 residues processed: 28 average time/residue: 0.1034 time to fit residues: 3.9104 Evaluate side-chains 25 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 18 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3138 r_free = 0.3138 target = 0.046017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.033292 restraints weight = 33149.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.034346 restraints weight = 16269.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.035053 restraints weight = 10549.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.035517 restraints weight = 8000.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035791 restraints weight = 6703.473| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5973 Z= 0.137 Angle : 0.631 7.384 8408 Z= 0.283 Chirality : 0.052 0.410 989 Planarity : 0.003 0.028 831 Dihedral : 14.829 173.546 1364 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.28 % Allowed : 10.26 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.91 (0.38), residues: 534 helix: 1.76 (0.57), residues: 97 sheet: 1.19 (0.39), residues: 171 loop : -0.19 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.009 0.001 TYR B 38 PHE 0.011 0.001 PHE A 166 TRP 0.007 0.001 TRP B 344 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 5973) covalent geometry : angle 0.63056 / 0.28 ( 8408) hydrogen bonds : bond 0.03441 / 2.24 ( 224) hydrogen bonds : angle 4.03534 / 2.72 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 95 SER cc_start: 0.9216 (t) cc_final: 0.8928 (p) REVERT: A 115 TYR cc_start: 0.9515 (t80) cc_final: 0.9309 (t80) REVERT: A 175 ILE cc_start: 0.9578 (mt) cc_final: 0.9246 (tp) REVERT: B 122 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8798 (ptpt) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.0921 time to fit residues: 3.3243 Evaluate side-chains 26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3079 r_free = 0.3079 target = 0.043884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031284 restraints weight = 34207.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032278 restraints weight = 16556.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.032964 restraints weight = 10824.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.033401 restraints weight = 8263.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.033618 restraints weight = 6982.514| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5973 Z= 0.291 Angle : 0.789 9.160 8408 Z= 0.358 Chirality : 0.055 0.427 989 Planarity : 0.003 0.033 831 Dihedral : 15.056 171.637 1364 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.92 % Allowed : 10.04 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.73 (0.38), residues: 534 helix: 1.91 (0.60), residues: 88 sheet: 0.96 (0.38), residues: 175 loop : -0.28 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.014 0.001 TYR B 38 PHE 0.009 0.002 PHE B 251 TRP 0.009 0.001 TRP A 206 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.29 ( 5973) covalent geometry : angle 0.78856 / 0.36 ( 8408) hydrogen bonds : bond 0.04861 / 3.12 ( 224) hydrogen bonds : angle 4.59941 / 3.11 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 19 time to evaluate : 0.159 Fit side-chains REVERT: A 95 SER cc_start: 0.9433 (t) cc_final: 0.9107 (p) REVERT: A 115 TYR cc_start: 0.9574 (t80) cc_final: 0.9353 (t80) REVERT: A 175 ILE cc_start: 0.9586 (mt) cc_final: 0.9263 (tp) REVERT: B 200 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8048 (mp10) outliers start: 9 outliers final: 6 residues processed: 28 average time/residue: 0.0841 time to fit residues: 3.2332 Evaluate side-chains 26 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3137 r_free = 0.3137 target = 0.045941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.033311 restraints weight = 32522.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.034380 restraints weight = 15962.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.035088 restraints weight = 10318.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035557 restraints weight = 7801.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035849 restraints weight = 6506.041| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5973 Z= 0.131 Angle : 0.654 7.860 8408 Z= 0.299 Chirality : 0.053 0.390 989 Planarity : 0.003 0.028 831 Dihedral : 14.848 172.721 1364 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.28 % Allowed : 10.90 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.38), residues: 534 helix: 1.60 (0.58), residues: 97 sheet: 1.08 (0.39), residues: 171 loop : -0.37 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 17 TYR 0.018 0.001 TYR B 38 PHE 0.012 0.001 PHE A 166 TRP 0.017 0.001 TRP B 344 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 5973) covalent geometry : angle 0.65433 / 0.30 ( 8408) hydrogen bonds : bond 0.03523 / 2.29 ( 224) hydrogen bonds : angle 4.17213 / 2.81 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 928.23 seconds wall clock time: 16 minutes 49.49 seconds (1009.49 seconds total)