Starting phenix.real_space_refine on Wed Feb 4 08:01:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.map" model { file = "/net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9od2_70338/02_2026/9od2_70338.cif" } resolution = 4.09 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5848 2.51 5 N 1588 2.21 5 O 1802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9304 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 914 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "A" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2922 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 Chain: "B" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2922 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 3 Time building chain proxies: 1.99, per 1000 atoms: 0.21 Number of scatterers: 9304 At special positions: 0 Unit cell: (160.02, 90.678, 85.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1802 8.00 N 1588 7.00 C 5848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS B 5 " distance=2.00 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 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: 0.46 Conformation dependent library (CDL) restraints added in 259.1 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 21 sheets defined 6.0% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.570A pdb=" N LYS A 395 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.919A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 261 through 269 Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.749A pdb=" N LEU C 82 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.638A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.695A pdb=" N PHE D 11 " --> pdb=" O THR D 105 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 91 Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.556A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.631A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.892A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 89 through 93 removed outlier: 3.590A pdb=" N MET L 92 " --> pdb=" O ILE L 95A" (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE L 95A" --> pdb=" O MET L 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 13 removed outlier: 3.722A pdb=" N VAL A 12 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 34 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 50 current: chain 'A' and resid 109 through 128 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 109 through 128 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 209 through 213 current: chain 'A' and resid 281 through 284 Processing sheet with id=AB3, first strand: chain 'A' and resid 21 through 26 removed outlier: 3.695A pdb=" N GLY A 187 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 243 through 248 removed outlier: 3.641A pdb=" N VAL A 256 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 312 through 313 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 312 through 313 current: chain 'A' and resid 326 through 332 Processing sheet with id=AB6, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AB8, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.532A pdb=" N VAL B 31 " --> pdb=" O ILE B 43 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 50 current: chain 'B' and resid 109 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 109 through 129 current: chain 'B' and resid 165 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 165 through 169 current: chain 'B' and resid 209 through 213 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 209 through 213 current: chain 'B' and resid 282 through 283 Processing sheet with id=AB9, first strand: chain 'B' and resid 21 through 25 removed outlier: 4.191A pdb=" N LYS B 290 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 248 removed outlier: 3.578A pdb=" N ALA B 248 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 320 removed outlier: 7.863A pdb=" N GLU B 329 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE B 317 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR B 327 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.620A pdb=" N GLN B 344 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 388 " --> pdb=" O GLN B 344 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3031 1.35 - 1.47: 2359 1.47 - 1.59: 4024 1.59 - 1.72: 0 1.72 - 1.84: 96 Bond restraints: 9510 Sorted by residual: bond pdb=" C CYS A 102 " pdb=" N ASN A 103 " ideal model delta sigma weight residual 1.333 1.311 0.022 1.49e-02 4.50e+03 2.17e+00 bond pdb=" CA TYR D 86 " pdb=" C TYR D 86 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.37e-02 5.33e+03 1.98e+00 bond pdb=" CB GLN H 43 " pdb=" CG GLN H 43 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB ARG B 299 " pdb=" CG ARG B 299 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CG GLN H 43 " pdb=" CD GLN H 43 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.49e+00 ... (remaining 9505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12621 1.89 - 3.77: 225 3.77 - 5.66: 41 5.66 - 7.55: 9 7.55 - 9.43: 4 Bond angle restraints: 12900 Sorted by residual: angle pdb=" C ALA A 361 " pdb=" N ASN A 362 " pdb=" CA ASN A 362 " ideal model delta sigma weight residual 121.80 131.23 -9.43 2.44e+00 1.68e-01 1.50e+01 angle pdb=" C THR H 28 " pdb=" N PHE H 29 " pdb=" CA PHE H 29 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA GLN B 89 " pdb=" CB GLN B 89 " pdb=" CG GLN B 89 " ideal model delta sigma weight residual 114.10 121.00 -6.90 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CB GLN H 43 " pdb=" CG GLN H 43 " pdb=" CD GLN H 43 " ideal model delta sigma weight residual 112.60 117.94 -5.34 1.70e+00 3.46e-01 9.86e+00 angle pdb=" CA MET A 349 " pdb=" CB MET A 349 " pdb=" CG MET A 349 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.61e+00 ... (remaining 12895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 5165 18.08 - 36.17: 388 36.17 - 54.25: 73 54.25 - 72.33: 12 72.33 - 90.41: 8 Dihedral angle restraints: 5646 sinusoidal: 2190 harmonic: 3456 Sorted by residual: dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -176.41 90.41 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " pdb=" SG CYS B 5 " pdb=" CB CYS B 5 " ideal model delta sinusoidal sigma weight residual 93.00 -179.38 -87.62 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS B 102 " pdb=" CB CYS B 102 " ideal model delta sinusoidal sigma weight residual -86.00 -160.66 74.66 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 5643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 955 0.037 - 0.073: 310 0.073 - 0.110: 129 0.110 - 0.147: 40 0.147 - 0.183: 2 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CA ASN A 362 " pdb=" N ASN A 362 " pdb=" C ASN A 362 " pdb=" CB ASN A 362 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB ILE D 66 " pdb=" CA ILE D 66 " pdb=" CG1 ILE D 66 " pdb=" CG2 ILE D 66 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CB THR B 335 " pdb=" CA THR B 335 " pdb=" OG1 THR B 335 " pdb=" CG2 THR B 335 " both_signs ideal model delta sigma weight residual False 2.55 2.69 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1433 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 170 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 171 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 52 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO H 52A" 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 52A" -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 52A" -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 100D" -0.011 2.00e-02 2.50e+03 1.12e-02 2.52e+00 pdb=" CG TYR C 100D" 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 100D" -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 100D" -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 100D" 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 100D" -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 100D" -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 100D" -0.001 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 676 2.74 - 3.28: 8379 3.28 - 3.82: 14880 3.82 - 4.36: 16120 4.36 - 4.90: 28695 Nonbonded interactions: 68750 Sorted by model distance: nonbonded pdb=" NE2 GLN B 89 " pdb=" O PHE B 119 " model vdw 2.200 3.120 nonbonded pdb=" O THR C 100B" pdb=" OG SER A 70 " model vdw 2.239 3.040 nonbonded pdb=" O TYR D 49 " pdb=" OG1 THR D 53 " model vdw 2.255 3.040 nonbonded pdb=" OG1 THR A 40 " pdb=" O ILE A 359 " model vdw 2.327 3.040 nonbonded pdb=" OG SER L 12 " pdb=" OG1 THR L 105 " model vdw 2.327 3.040 ... (remaining 68745 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.100 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.039 9528 Z= 0.135 Angle : 0.663 11.550 12936 Z= 0.344 Chirality : 0.045 0.183 1436 Planarity : 0.004 0.043 1650 Dihedral : 13.165 89.610 3396 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.10 % Allowed : 0.49 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1198 helix: -1.94 (0.76), residues: 28 sheet: 0.48 (0.24), residues: 497 loop : -0.31 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.028 0.002 TYR C 100D PHE 0.012 0.001 PHE B 314 TRP 0.028 0.002 TRP C 47 HIS 0.003 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9510) covalent geometry : angle 0.65176 (12900) SS BOND : bond 0.00803 ( 18) SS BOND : angle 2.36966 ( 36) hydrogen bonds : bond 0.26772 ( 203) hydrogen bonds : angle 9.94973 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7656 (tp30) cc_final: 0.7437 (mm-30) REVERT: A 20 TRP cc_start: 0.8414 (m100) cc_final: 0.8158 (m100) REVERT: A 225 TRP cc_start: 0.8334 (p-90) cc_final: 0.8055 (p-90) REVERT: B 45 LEU cc_start: 0.8246 (tp) cc_final: 0.8004 (pt) REVERT: B 225 TRP cc_start: 0.8275 (p-90) cc_final: 0.7929 (p-90) REVERT: B 345 MET cc_start: 0.5606 (tpp) cc_final: 0.5186 (tpp) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.0746 time to fit residues: 17.8447 Evaluate side-chains 128 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 ASN A 253 GLN B 344 GLN B 362 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.096003 restraints weight = 24335.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.097597 restraints weight = 14941.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098763 restraints weight = 11667.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.098799 restraints weight = 9349.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.099191 restraints weight = 9218.615| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9528 Z= 0.192 Angle : 0.579 6.494 12936 Z= 0.309 Chirality : 0.044 0.195 1436 Planarity : 0.004 0.034 1650 Dihedral : 4.257 23.377 1310 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: -0.07 (0.25), residues: 1198 helix: -1.16 (0.93), residues: 28 sheet: 0.43 (0.24), residues: 474 loop : -0.27 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 83 TYR 0.023 0.002 TYR C 100D PHE 0.014 0.002 PHE L 98 TRP 0.023 0.002 TRP H 103 HIS 0.007 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9510) covalent geometry : angle 0.57851 (12900) SS BOND : bond 0.00415 ( 18) SS BOND : angle 0.70703 ( 36) hydrogen bonds : bond 0.03944 ( 203) hydrogen bonds : angle 7.44608 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7787 (tp30) cc_final: 0.7359 (tp30) REVERT: H 72 ASP cc_start: 0.8360 (t70) cc_final: 0.8140 (t0) REVERT: H 85 GLU cc_start: 0.7836 (pm20) cc_final: 0.7596 (pm20) REVERT: L 104 LEU cc_start: 0.7202 (tp) cc_final: 0.6595 (tp) REVERT: A 206 MET cc_start: 0.6611 (tmm) cc_final: 0.6091 (ptt) REVERT: A 225 TRP cc_start: 0.8384 (p-90) cc_final: 0.7982 (p-90) REVERT: B 45 LEU cc_start: 0.8376 (tp) cc_final: 0.8127 (pt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0756 time to fit residues: 16.3542 Evaluate side-chains 114 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 113 optimal weight: 0.0070 chunk 64 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 37 GLN L 6 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 362 ASN B 371 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.127780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098375 restraints weight = 24154.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.100330 restraints weight = 15433.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.101271 restraints weight = 11899.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.101561 restraints weight = 9199.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.102061 restraints weight = 8773.934| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9528 Z= 0.128 Angle : 0.525 7.041 12936 Z= 0.279 Chirality : 0.044 0.216 1436 Planarity : 0.003 0.032 1650 Dihedral : 4.066 22.635 1310 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: -0.01 (0.25), residues: 1198 helix: -0.91 (0.98), residues: 28 sheet: 0.49 (0.24), residues: 471 loop : -0.27 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 164 TYR 0.024 0.002 TYR C 97 PHE 0.007 0.001 PHE B 108 TRP 0.016 0.001 TRP H 103 HIS 0.004 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9510) covalent geometry : angle 0.52295 (12900) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.96038 ( 36) hydrogen bonds : bond 0.03635 ( 203) hydrogen bonds : angle 6.94335 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7857 (tp30) cc_final: 0.7421 (tp30) REVERT: H 72 ASP cc_start: 0.8480 (t70) cc_final: 0.8029 (t0) REVERT: H 85 GLU cc_start: 0.7807 (pm20) cc_final: 0.7556 (pm20) REVERT: L 104 LEU cc_start: 0.7261 (tp) cc_final: 0.6818 (tp) REVERT: A 225 TRP cc_start: 0.8345 (p-90) cc_final: 0.7974 (p-90) REVERT: B 45 LEU cc_start: 0.8328 (tp) cc_final: 0.8093 (pt) REVERT: B 206 MET cc_start: 0.6100 (ptm) cc_final: 0.5804 (ptt) REVERT: B 225 TRP cc_start: 0.8330 (p-90) cc_final: 0.7921 (p-90) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0753 time to fit residues: 16.6788 Evaluate side-chains 118 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 65 optimal weight: 0.0570 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN B 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.123375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.093057 restraints weight = 25166.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094648 restraints weight = 16337.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.095438 restraints weight = 12875.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.096508 restraints weight = 10411.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096730 restraints weight = 9489.815| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9528 Z= 0.224 Angle : 0.627 6.794 12936 Z= 0.335 Chirality : 0.045 0.199 1436 Planarity : 0.004 0.032 1650 Dihedral : 4.645 27.801 1310 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 (0.25), residues: 1198 helix: -1.56 (0.81), residues: 28 sheet: 0.19 (0.24), residues: 464 loop : -0.44 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 283 TYR 0.028 0.003 TYR C 100D PHE 0.014 0.002 PHE B 108 TRP 0.022 0.002 TRP C 103 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 9510) covalent geometry : angle 0.62591 (12900) SS BOND : bond 0.00403 ( 18) SS BOND : angle 0.90184 ( 36) hydrogen bonds : bond 0.03763 ( 203) hydrogen bonds : angle 6.88961 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7650 (tp30) cc_final: 0.7188 (tp30) REVERT: H 72 ASP cc_start: 0.8552 (t70) cc_final: 0.8180 (t0) REVERT: H 85 GLU cc_start: 0.7956 (pm20) cc_final: 0.7650 (pm20) REVERT: L 105 THR cc_start: 0.7651 (p) cc_final: 0.6432 (p) REVERT: A 331 GLN cc_start: 0.7593 (tt0) cc_final: 0.7353 (mp10) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0799 time to fit residues: 15.9255 Evaluate side-chains 106 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 14 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.127354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098343 restraints weight = 25345.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.099470 restraints weight = 16099.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100876 restraints weight = 12936.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.101159 restraints weight = 10581.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.101606 restraints weight = 10745.409| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9528 Z= 0.118 Angle : 0.530 7.048 12936 Z= 0.280 Chirality : 0.044 0.221 1436 Planarity : 0.003 0.030 1650 Dihedral : 4.227 23.779 1310 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.32 (0.25), residues: 1198 helix: -0.85 (0.91), residues: 28 sheet: 0.17 (0.24), residues: 470 loop : -0.40 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.024 0.002 TYR C 97 PHE 0.008 0.001 PHE L 62 TRP 0.016 0.001 TRP H 103 HIS 0.003 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9510) covalent geometry : angle 0.52917 (12900) SS BOND : bond 0.00487 ( 18) SS BOND : angle 0.76343 ( 36) hydrogen bonds : bond 0.03244 ( 203) hydrogen bonds : angle 6.42952 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7609 (tp30) cc_final: 0.7246 (tp30) REVERT: H 72 ASP cc_start: 0.8461 (t70) cc_final: 0.8230 (t0) REVERT: H 85 GLU cc_start: 0.7864 (pm20) cc_final: 0.7574 (pm20) REVERT: L 104 LEU cc_start: 0.7419 (tp) cc_final: 0.6560 (tt) REVERT: B 225 TRP cc_start: 0.8396 (p-90) cc_final: 0.8053 (p-90) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0827 time to fit residues: 17.8172 Evaluate side-chains 112 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 80 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.095919 restraints weight = 24529.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.098204 restraints weight = 15393.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.098926 restraints weight = 11151.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099299 restraints weight = 9379.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.099548 restraints weight = 9053.794| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9528 Z= 0.139 Angle : 0.551 9.203 12936 Z= 0.289 Chirality : 0.044 0.182 1436 Planarity : 0.003 0.031 1650 Dihedral : 4.206 24.669 1310 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: -0.27 (0.25), residues: 1198 helix: -0.51 (0.96), residues: 28 sheet: 0.28 (0.24), residues: 469 loop : -0.44 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.025 0.002 TYR C 100D PHE 0.009 0.001 PHE B 108 TRP 0.016 0.001 TRP H 103 HIS 0.004 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9510) covalent geometry : angle 0.55002 (12900) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.83166 ( 36) hydrogen bonds : bond 0.03179 ( 203) hydrogen bonds : angle 6.36724 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7742 (tp30) cc_final: 0.7324 (tp30) REVERT: H 72 ASP cc_start: 0.8480 (t70) cc_final: 0.8159 (t0) REVERT: H 85 GLU cc_start: 0.7881 (pm20) cc_final: 0.7551 (pm20) REVERT: L 104 LEU cc_start: 0.7609 (tp) cc_final: 0.6305 (tt) REVERT: A 295 MET cc_start: 0.6305 (mpp) cc_final: 0.5637 (mpp) REVERT: B 61 TYR cc_start: 0.6831 (m-10) cc_final: 0.6346 (m-10) REVERT: B 225 TRP cc_start: 0.8357 (p-90) cc_final: 0.7951 (p-90) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0798 time to fit residues: 16.8899 Evaluate side-chains 117 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.124213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.094018 restraints weight = 24833.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095874 restraints weight = 15627.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096656 restraints weight = 11981.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097616 restraints weight = 9867.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.097805 restraints weight = 9285.259| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9528 Z= 0.188 Angle : 0.594 6.806 12936 Z= 0.315 Chirality : 0.045 0.193 1436 Planarity : 0.004 0.033 1650 Dihedral : 4.498 24.756 1310 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.36 (0.25), residues: 1198 helix: -1.00 (0.93), residues: 28 sheet: 0.29 (0.24), residues: 464 loop : -0.53 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 283 TYR 0.035 0.003 TYR C 100D PHE 0.012 0.002 PHE B 108 TRP 0.016 0.002 TRP H 103 HIS 0.006 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9510) covalent geometry : angle 0.59286 (12900) SS BOND : bond 0.00380 ( 18) SS BOND : angle 0.86536 ( 36) hydrogen bonds : bond 0.03458 ( 203) hydrogen bonds : angle 6.54669 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7568 (tp30) cc_final: 0.7123 (tp30) REVERT: H 72 ASP cc_start: 0.8531 (t70) cc_final: 0.8214 (t0) REVERT: H 85 GLU cc_start: 0.7929 (pm20) cc_final: 0.7601 (pm20) REVERT: L 104 LEU cc_start: 0.7773 (tp) cc_final: 0.6412 (tt) REVERT: A 189 ASP cc_start: 0.7983 (p0) cc_final: 0.7589 (m-30) REVERT: A 295 MET cc_start: 0.6292 (mpp) cc_final: 0.5655 (mpp) REVERT: B 61 TYR cc_start: 0.6814 (m-10) cc_final: 0.6102 (m-10) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0816 time to fit residues: 16.4164 Evaluate side-chains 110 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.095880 restraints weight = 24386.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097491 restraints weight = 15285.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.098273 restraints weight = 11736.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.098626 restraints weight = 9858.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098947 restraints weight = 9511.516| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9528 Z= 0.131 Angle : 0.546 6.891 12936 Z= 0.289 Chirality : 0.044 0.195 1436 Planarity : 0.003 0.031 1650 Dihedral : 4.275 26.707 1310 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.40 (0.25), residues: 1198 helix: -0.55 (0.97), residues: 28 sheet: 0.18 (0.24), residues: 461 loop : -0.52 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.023 0.002 TYR H 98 PHE 0.007 0.001 PHE A 312 TRP 0.016 0.002 TRP H 103 HIS 0.004 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9510) covalent geometry : angle 0.54499 (12900) SS BOND : bond 0.00282 ( 18) SS BOND : angle 0.77549 ( 36) hydrogen bonds : bond 0.03106 ( 203) hydrogen bonds : angle 6.29131 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7483 (tp30) cc_final: 0.7091 (tp30) REVERT: H 72 ASP cc_start: 0.8530 (t70) cc_final: 0.8249 (t0) REVERT: H 85 GLU cc_start: 0.7924 (pm20) cc_final: 0.7578 (pm20) REVERT: L 104 LEU cc_start: 0.7773 (tp) cc_final: 0.6536 (tt) REVERT: A 189 ASP cc_start: 0.8115 (p0) cc_final: 0.7647 (m-30) REVERT: A 295 MET cc_start: 0.6400 (mpp) cc_final: 0.5853 (mpp) REVERT: B 61 TYR cc_start: 0.6723 (m-10) cc_final: 0.6519 (m-80) REVERT: B 125 MET cc_start: 0.7889 (ptp) cc_final: 0.7659 (ptp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0807 time to fit residues: 16.2261 Evaluate side-chains 114 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.0870 chunk 4 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 0.0270 chunk 6 optimal weight: 0.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.128321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098769 restraints weight = 24990.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100588 restraints weight = 16321.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.101331 restraints weight = 12514.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.103030 restraints weight = 9910.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103068 restraints weight = 8336.144| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9528 Z= 0.091 Angle : 0.526 7.635 12936 Z= 0.272 Chirality : 0.044 0.186 1436 Planarity : 0.003 0.031 1650 Dihedral : 3.921 24.246 1310 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.18 (0.25), residues: 1198 helix: 0.13 (1.04), residues: 28 sheet: 0.42 (0.26), residues: 425 loop : -0.42 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.018 0.001 TYR H 98 PHE 0.008 0.001 PHE H 29 TRP 0.016 0.001 TRP H 103 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9510) covalent geometry : angle 0.52512 (12900) SS BOND : bond 0.00209 ( 18) SS BOND : angle 0.71884 ( 36) hydrogen bonds : bond 0.02970 ( 203) hydrogen bonds : angle 5.96476 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7655 (tp30) cc_final: 0.7235 (tp30) REVERT: H 72 ASP cc_start: 0.8331 (t70) cc_final: 0.8039 (t0) REVERT: H 85 GLU cc_start: 0.7861 (pm20) cc_final: 0.7553 (pm20) REVERT: L 104 LEU cc_start: 0.7558 (tp) cc_final: 0.6782 (tt) REVERT: A 180 LEU cc_start: 0.9045 (mp) cc_final: 0.8842 (tt) REVERT: A 189 ASP cc_start: 0.8008 (p0) cc_final: 0.7594 (m-30) REVERT: A 295 MET cc_start: 0.6272 (mpp) cc_final: 0.5695 (mpp) REVERT: B 125 MET cc_start: 0.7699 (ptp) cc_final: 0.7471 (ptp) REVERT: B 225 TRP cc_start: 0.8297 (p-90) cc_final: 0.7918 (p-90) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0819 time to fit residues: 18.5491 Evaluate side-chains 122 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 0.0070 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 70 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.126939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.096873 restraints weight = 24692.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.098049 restraints weight = 15911.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.099200 restraints weight = 12286.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099295 restraints weight = 9872.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099662 restraints weight = 9865.088| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9528 Z= 0.114 Angle : 0.534 6.824 12936 Z= 0.280 Chirality : 0.043 0.181 1436 Planarity : 0.003 0.030 1650 Dihedral : 3.948 24.934 1310 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.15 (0.25), residues: 1198 helix: 0.18 (1.06), residues: 28 sheet: 0.46 (0.26), residues: 416 loop : -0.41 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.025 0.002 TYR C 100D PHE 0.010 0.001 PHE A 312 TRP 0.015 0.001 TRP H 103 HIS 0.003 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9510) covalent geometry : angle 0.53398 (12900) SS BOND : bond 0.00247 ( 18) SS BOND : angle 0.66161 ( 36) hydrogen bonds : bond 0.02996 ( 203) hydrogen bonds : angle 5.90168 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7576 (tp30) cc_final: 0.7207 (tp30) REVERT: H 72 ASP cc_start: 0.8383 (t70) cc_final: 0.8099 (t0) REVERT: H 85 GLU cc_start: 0.7940 (pm20) cc_final: 0.7596 (pm20) REVERT: L 104 LEU cc_start: 0.7775 (tp) cc_final: 0.6683 (tt) REVERT: A 180 LEU cc_start: 0.9070 (mp) cc_final: 0.8867 (tt) REVERT: A 189 ASP cc_start: 0.8136 (p0) cc_final: 0.7702 (m-30) REVERT: A 295 MET cc_start: 0.6471 (mpp) cc_final: 0.5912 (mpp) REVERT: B 61 TYR cc_start: 0.6614 (m-10) cc_final: 0.5998 (m-80) REVERT: B 125 MET cc_start: 0.7900 (ptp) cc_final: 0.7664 (ptp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0830 time to fit residues: 17.8136 Evaluate side-chains 113 residues out of total 1012 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 118 optimal weight: 0.2980 chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.127377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.096512 restraints weight = 24007.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099007 restraints weight = 14456.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101545 restraints weight = 10040.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.101284 restraints weight = 7768.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.101487 restraints weight = 7686.712| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9528 Z= 0.110 Angle : 0.531 6.834 12936 Z= 0.277 Chirality : 0.043 0.180 1436 Planarity : 0.003 0.031 1650 Dihedral : 3.948 23.888 1310 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % 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: -0.14 (0.25), residues: 1198 helix: 0.15 (1.05), residues: 28 sheet: 0.33 (0.25), residues: 433 loop : -0.31 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 99 TYR 0.024 0.002 TYR C 100D PHE 0.009 0.001 PHE A 312 TRP 0.015 0.001 TRP H 103 HIS 0.002 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9510) covalent geometry : angle 0.53048 (12900) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.65706 ( 36) hydrogen bonds : bond 0.03020 ( 203) hydrogen bonds : angle 5.84319 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1455.96 seconds wall clock time: 26 minutes 0.51 seconds (1560.51 seconds total)