Starting phenix.real_space_refine on Wed Feb 4 01:38:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.map" model { file = "/net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz5_66382/02_2026/9wz5_66382.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 24 5.16 5 C 5292 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 8256 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.02, per 1000 atoms: 0.24 Number of scatterers: 8256 At special positions: 0 Unit cell: (90.1, 89.25, 94.35, 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 24 16.00 O 1500 8.00 N 1440 7.00 C 5292 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: 0.82 Conformation dependent library (CDL) restraints added in 299.4 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.013A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.080A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.536A pdb=" N ALA A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.648A pdb=" N VAL A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.024A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.571A pdb=" N VAL B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.996A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 151 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 165 through 169 removed outlier: 3.508A pdb=" N ALA C 168 " --> pdb=" O PHE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.581A pdb=" N VAL C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.067A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.580A pdb=" N ALA D 168 " --> pdb=" O PHE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 185 through 194 removed outlier: 3.761A pdb=" N VAL D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.067A pdb=" N LEU E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 3.533A pdb=" N ALA E 168 " --> pdb=" O PHE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 Processing helix chain 'E' and resid 185 through 194 removed outlier: 3.669A pdb=" N VAL E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 137 removed outlier: 3.991A pdb=" N LEU F 132 " --> pdb=" O ASN F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 170 through 185 Processing helix chain 'F' and resid 185 through 194 removed outlier: 3.650A pdb=" N VAL F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 126 Processing helix chain 'G' and resid 128 through 137 removed outlier: 4.062A pdb=" N LEU G 132 " --> pdb=" O ASN G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 165 through 169 removed outlier: 3.550A pdb=" N ALA G 168 " --> pdb=" O PHE G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 185 Processing helix chain 'G' and resid 185 through 194 removed outlier: 3.509A pdb=" N VAL G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 126 Processing helix chain 'H' and resid 128 through 137 removed outlier: 4.025A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 165 through 169 removed outlier: 3.545A pdb=" N ALA H 168 " --> pdb=" O PHE H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 185 Processing helix chain 'H' and resid 185 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 126 Processing helix chain 'I' and resid 128 through 137 removed outlier: 4.030A pdb=" N LEU I 132 " --> pdb=" O ASN I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 170 through 185 Processing helix chain 'I' and resid 185 through 194 removed outlier: 3.884A pdb=" N VAL I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 126 Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.061A pdb=" N LEU J 132 " --> pdb=" O ASN J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 151 Processing helix chain 'J' and resid 154 through 164 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 170 through 185 Processing helix chain 'J' and resid 185 through 194 removed outlier: 3.619A pdb=" N VAL J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 Processing helix chain 'K' and resid 128 through 137 removed outlier: 4.062A pdb=" N LEU K 132 " --> pdb=" O ASN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 165 through 169 removed outlier: 3.532A pdb=" N ALA K 168 " --> pdb=" O PHE K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 185 Processing helix chain 'K' and resid 185 through 194 removed outlier: 3.780A pdb=" N VAL K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 126 Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.065A pdb=" N LEU L 132 " --> pdb=" O ASN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 151 Processing helix chain 'L' and resid 154 through 164 Processing helix chain 'L' and resid 165 through 169 removed outlier: 3.547A pdb=" N ALA L 168 " --> pdb=" O PHE L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 185 Processing helix chain 'L' and resid 185 through 194 removed outlier: 3.559A pdb=" N VAL L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1515 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: 1.06 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2683 1.34 - 1.46: 1289 1.46 - 1.57: 4440 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 8448 Sorted by residual: bond pdb=" N GLU L 144 " pdb=" CA GLU L 144 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.67e+00 bond pdb=" C GLU L 144 " pdb=" O GLU L 144 " ideal model delta sigma weight residual 1.237 1.227 0.010 1.19e-02 7.06e+03 6.84e-01 bond pdb=" CA THR I 166 " pdb=" C THR I 166 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.26e-02 6.30e+03 6.30e-01 bond pdb=" C THR L 166 " pdb=" N PRO L 167 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.41e-01 bond pdb=" CB ARG J 150 " pdb=" CG ARG J 150 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.15e-01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11292 2.07 - 4.14: 121 4.14 - 6.22: 37 6.22 - 8.29: 10 8.29 - 10.36: 12 Bond angle restraints: 11472 Sorted by residual: angle pdb=" N VAL G 140 " pdb=" CA VAL G 140 " pdb=" C VAL G 140 " ideal model delta sigma weight residual 113.53 108.42 5.11 9.80e-01 1.04e+00 2.72e+01 angle pdb=" N VAL H 140 " pdb=" CA VAL H 140 " pdb=" C VAL H 140 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" C PHE I 165 " pdb=" N THR I 166 " pdb=" CA THR I 166 " ideal model delta sigma weight residual 120.09 125.54 -5.45 1.25e+00 6.40e-01 1.90e+01 angle pdb=" C PHE D 165 " pdb=" N THR D 166 " pdb=" CA THR D 166 " ideal model delta sigma weight residual 120.06 124.83 -4.77 1.19e+00 7.06e-01 1.61e+01 angle pdb=" N THR K 166 " pdb=" CA THR K 166 " pdb=" C THR K 166 " ideal model delta sigma weight residual 109.81 116.62 -6.81 2.21e+00 2.05e-01 9.49e+00 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 4548 16.55 - 33.10: 364 33.10 - 49.66: 133 49.66 - 66.21: 17 66.21 - 82.76: 14 Dihedral angle restraints: 5076 sinusoidal: 2088 harmonic: 2988 Sorted by residual: dihedral pdb=" CG ARG L 150 " pdb=" CD ARG L 150 " pdb=" NE ARG L 150 " pdb=" CZ ARG L 150 " ideal model delta sinusoidal sigma weight residual 180.00 135.67 44.33 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG K 150 " pdb=" CD ARG K 150 " pdb=" NE ARG K 150 " pdb=" CZ ARG K 150 " ideal model delta sinusoidal sigma weight residual 180.00 135.71 44.29 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG G 150 " pdb=" CD ARG G 150 " pdb=" NE ARG G 150 " pdb=" CZ ARG G 150 " ideal model delta sinusoidal sigma weight residual 180.00 136.23 43.77 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 823 0.029 - 0.058: 323 0.058 - 0.088: 31 0.088 - 0.117: 83 0.117 - 0.146: 12 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA THR K 166 " pdb=" N THR K 166 " pdb=" C THR K 166 " pdb=" CB THR K 166 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA THR B 166 " pdb=" N THR B 166 " pdb=" C THR B 166 " pdb=" CB THR B 166 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA THR F 166 " pdb=" N THR F 166 " pdb=" C THR F 166 " pdb=" CB THR F 166 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 166 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO K 167 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO K 167 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 167 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 166 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 167 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 166 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO J 167 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO J 167 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO J 167 " 0.024 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2138 2.82 - 3.34: 7493 3.34 - 3.86: 13179 3.86 - 4.38: 15517 4.38 - 4.90: 28196 Nonbonded interactions: 66523 Sorted by model distance: nonbonded pdb=" O PHE E 163 " pdb=" OG1 THR E 166 " model vdw 2.295 3.040 nonbonded pdb=" OE2 GLU G 144 " pdb=" NH2 ARG H 160 " model vdw 2.312 3.120 nonbonded pdb=" NH2 ARG C 160 " pdb=" OE2 GLU H 144 " model vdw 2.313 3.120 nonbonded pdb=" OE2 GLU D 144 " pdb=" NH2 ARG K 160 " model vdw 2.322 3.120 nonbonded pdb=" OE2 GLU A 144 " pdb=" NH2 ARG G 160 " model vdw 2.324 3.120 ... (remaining 66518 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.010 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.004 0.034 8448 Z= 0.158 Angle : 0.663 10.359 11472 Z= 0.330 Chirality : 0.040 0.146 1272 Planarity : 0.005 0.043 1452 Dihedral : 14.421 82.762 3108 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.46 (0.28), residues: 972 helix: 1.69 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -2.37 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 150 TYR 0.015 0.002 TYR H 146 PHE 0.011 0.001 PHE E 114 TRP 0.006 0.001 TRP D 171 HIS 0.006 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8448) covalent geometry : angle 0.66260 (11472) hydrogen bonds : bond 0.17487 ( 521) hydrogen bonds : angle 4.30133 ( 1515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.352 Fit side-chains REVERT: B 191 ASP cc_start: 0.8138 (t70) cc_final: 0.7938 (t0) REVERT: K 179 GLN cc_start: 0.7945 (tp40) cc_final: 0.6734 (tp-100) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.7163 time to fit residues: 223.9102 Evaluate side-chains 240 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 147 GLN D 147 GLN E 128 ASN G 147 GLN H 147 GLN H 185 GLN J 128 ASN K 128 ASN L 179 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.056955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.048469 restraints weight = 20079.626| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 2.92 r_work: 0.2298 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8448 Z= 0.114 Angle : 0.564 7.317 11472 Z= 0.280 Chirality : 0.037 0.128 1272 Planarity : 0.005 0.043 1452 Dihedral : 3.248 11.012 1092 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.82 % Allowed : 12.50 % Favored : 84.68 % 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: 2.52 (0.29), residues: 972 helix: 2.33 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.81 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 194 TYR 0.011 0.001 TYR A 146 PHE 0.010 0.001 PHE K 114 TRP 0.004 0.000 TRP I 169 HIS 0.002 0.001 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8448) covalent geometry : angle 0.56426 (11472) hydrogen bonds : bond 0.02808 ( 521) hydrogen bonds : angle 3.29028 ( 1515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 0.306 Fit side-chains REVERT: B 147 GLN cc_start: 0.8962 (mt0) cc_final: 0.8699 (mt0) REVERT: B 191 ASP cc_start: 0.9128 (t70) cc_final: 0.8651 (t0) REVERT: C 191 ASP cc_start: 0.9110 (t0) cc_final: 0.8894 (t0) REVERT: D 130 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5450 (tt0) REVERT: D 179 GLN cc_start: 0.8985 (tp40) cc_final: 0.8633 (tm-30) REVERT: D 183 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 190 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 179 GLN cc_start: 0.8747 (mm-40) cc_final: 0.7864 (tp-100) REVERT: E 183 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8143 (mp0) REVERT: F 191 ASP cc_start: 0.9091 (t0) cc_final: 0.8841 (t0) REVERT: G 191 ASP cc_start: 0.9186 (t0) cc_final: 0.8931 (t0) REVERT: H 191 ASP cc_start: 0.9217 (t0) cc_final: 0.9012 (t0) REVERT: I 179 GLN cc_start: 0.8881 (tp40) cc_final: 0.8270 (tm-30) REVERT: I 191 ASP cc_start: 0.9058 (t0) cc_final: 0.8767 (t0) REVERT: J 130 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8500 (mm-30) REVERT: J 191 ASP cc_start: 0.9089 (t0) cc_final: 0.8739 (t0) REVERT: K 183 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: L 191 ASP cc_start: 0.9167 (t0) cc_final: 0.8953 (t0) outliers start: 25 outliers final: 12 residues processed: 266 average time/residue: 0.6602 time to fit residues: 183.9561 Evaluate side-chains 245 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 231 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 183 GLU Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN D 147 GLN G 147 GLN H 147 GLN J 147 GLN K 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.056732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.047629 restraints weight = 19480.890| |-----------------------------------------------------------------------------| r_work (start): 0.2431 rms_B_bonded: 2.92 r_work: 0.2261 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.129 Angle : 0.547 5.974 11472 Z= 0.276 Chirality : 0.037 0.127 1272 Planarity : 0.005 0.047 1452 Dihedral : 3.213 11.055 1092 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % 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: 3.05 (0.29), residues: 972 helix: 2.68 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.51 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 194 TYR 0.017 0.001 TYR H 146 PHE 0.011 0.001 PHE K 114 TRP 0.002 0.000 TRP A 169 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8448) covalent geometry : angle 0.54667 (11472) hydrogen bonds : bond 0.03104 ( 521) hydrogen bonds : angle 3.16380 ( 1515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.299 Fit side-chains REVERT: B 191 ASP cc_start: 0.9148 (t70) cc_final: 0.8684 (t0) REVERT: C 191 ASP cc_start: 0.9156 (t0) cc_final: 0.8951 (t0) REVERT: D 179 GLN cc_start: 0.9009 (tp40) cc_final: 0.8691 (tm-30) REVERT: D 183 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 190 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8422 (mm-30) REVERT: E 143 ASP cc_start: 0.8349 (t70) cc_final: 0.8104 (t70) REVERT: E 147 GLN cc_start: 0.8806 (mt0) cc_final: 0.8553 (mt0) REVERT: F 147 GLN cc_start: 0.9043 (mt0) cc_final: 0.8841 (mt0) REVERT: G 191 ASP cc_start: 0.9155 (t0) cc_final: 0.8908 (t0) REVERT: I 179 GLN cc_start: 0.8992 (tp40) cc_final: 0.8399 (tm-30) REVERT: I 191 ASP cc_start: 0.9051 (t0) cc_final: 0.8742 (t0) REVERT: J 130 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8510 (mm-30) REVERT: J 191 ASP cc_start: 0.9106 (t0) cc_final: 0.8753 (t0) REVERT: K 130 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5655 (tt0) REVERT: K 147 GLN cc_start: 0.8903 (mt0) cc_final: 0.8660 (mt0) REVERT: L 191 ASP cc_start: 0.9204 (t0) cc_final: 0.8991 (t0) outliers start: 23 outliers final: 12 residues processed: 254 average time/residue: 0.6901 time to fit residues: 183.2263 Evaluate side-chains 246 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN D 147 GLN E 179 GLN G 147 GLN H 147 GLN K 179 GLN L 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.048623 restraints weight = 19740.272| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 3.01 r_work: 0.2323 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8448 Z= 0.112 Angle : 0.582 9.722 11472 Z= 0.281 Chirality : 0.036 0.128 1272 Planarity : 0.005 0.047 1452 Dihedral : 3.112 10.823 1092 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.27 % Allowed : 16.44 % Favored : 80.29 % 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: 3.13 (0.29), residues: 972 helix: 2.72 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.39 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 194 TYR 0.014 0.001 TYR H 146 PHE 0.011 0.001 PHE F 114 TRP 0.002 0.000 TRP J 169 HIS 0.002 0.000 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8448) covalent geometry : angle 0.58235 (11472) hydrogen bonds : bond 0.02487 ( 521) hydrogen bonds : angle 3.11690 ( 1515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.244 Fit side-chains REVERT: B 191 ASP cc_start: 0.9203 (t70) cc_final: 0.8764 (t0) REVERT: C 191 ASP cc_start: 0.9245 (t0) cc_final: 0.8963 (t0) REVERT: D 130 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.5705 (tt0) REVERT: D 179 GLN cc_start: 0.9148 (tp40) cc_final: 0.8656 (tm-30) REVERT: D 183 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 190 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8444 (mm-30) REVERT: D 191 ASP cc_start: 0.9081 (t0) cc_final: 0.8844 (t0) REVERT: F 179 GLN cc_start: 0.8764 (tp40) cc_final: 0.8545 (tm-30) REVERT: G 191 ASP cc_start: 0.9218 (t0) cc_final: 0.8964 (t0) REVERT: I 130 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5788 (tt0) REVERT: I 179 GLN cc_start: 0.9087 (tp40) cc_final: 0.8170 (tp-100) REVERT: I 191 ASP cc_start: 0.9142 (t0) cc_final: 0.8901 (t0) REVERT: J 130 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8596 (mm-30) REVERT: J 191 ASP cc_start: 0.9163 (t0) cc_final: 0.8821 (t0) REVERT: K 130 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5818 (tt0) REVERT: K 179 GLN cc_start: 0.8975 (tp40) cc_final: 0.8699 (tm-30) REVERT: K 183 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: K 191 ASP cc_start: 0.8957 (t0) cc_final: 0.8730 (t0) REVERT: L 191 ASP cc_start: 0.9277 (t0) cc_final: 0.8871 (t0) outliers start: 29 outliers final: 14 residues processed: 263 average time/residue: 0.6866 time to fit residues: 188.9696 Evaluate side-chains 255 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN E 179 GLN G 147 GLN H 147 GLN L 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.056813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.047721 restraints weight = 19460.847| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 2.98 r_work: 0.2304 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.123 Angle : 0.628 10.466 11472 Z= 0.293 Chirality : 0.038 0.124 1272 Planarity : 0.005 0.049 1452 Dihedral : 3.130 10.973 1092 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.36 % Allowed : 19.37 % Favored : 78.27 % 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: 3.17 (0.29), residues: 972 helix: 2.75 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 194 TYR 0.018 0.001 TYR H 146 PHE 0.009 0.001 PHE D 114 TRP 0.002 0.000 TRP C 171 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8448) covalent geometry : angle 0.62835 (11472) hydrogen bonds : bond 0.02740 ( 521) hydrogen bonds : angle 3.10164 ( 1515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.418 Fit side-chains REVERT: B 139 LYS cc_start: 0.9542 (mtmm) cc_final: 0.9332 (mttm) REVERT: B 147 GLN cc_start: 0.9130 (mt0) cc_final: 0.8927 (mt0) REVERT: B 191 ASP cc_start: 0.9212 (t70) cc_final: 0.8708 (t0) REVERT: C 191 ASP cc_start: 0.9218 (t0) cc_final: 0.8999 (t0) REVERT: D 179 GLN cc_start: 0.9170 (tp40) cc_final: 0.8718 (tm-30) REVERT: D 183 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7841 (mt-10) REVERT: D 190 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8522 (mm-30) REVERT: E 147 GLN cc_start: 0.8912 (mt0) cc_final: 0.8601 (mt0) REVERT: F 179 GLN cc_start: 0.8850 (tp40) cc_final: 0.8552 (tm-30) REVERT: G 191 ASP cc_start: 0.9231 (t0) cc_final: 0.8974 (t0) REVERT: I 130 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5831 (tt0) REVERT: I 179 GLN cc_start: 0.9103 (tp40) cc_final: 0.8235 (tp-100) REVERT: I 191 ASP cc_start: 0.9149 (t0) cc_final: 0.8697 (t0) REVERT: J 130 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8574 (mm-30) REVERT: J 147 GLN cc_start: 0.9009 (mt0) cc_final: 0.8809 (mt0) REVERT: J 191 ASP cc_start: 0.9199 (t0) cc_final: 0.8838 (t0) REVERT: K 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8774 (mt0) REVERT: K 179 GLN cc_start: 0.9038 (tp40) cc_final: 0.8649 (tm-30) REVERT: K 183 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: L 191 ASP cc_start: 0.9273 (t0) cc_final: 0.8881 (t0) outliers start: 21 outliers final: 13 residues processed: 250 average time/residue: 0.6047 time to fit residues: 158.0569 Evaluate side-chains 249 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 186 SER Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN E 179 GLN F 147 GLN G 147 GLN H 147 GLN J 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.058358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.049215 restraints weight = 19285.192| |-----------------------------------------------------------------------------| r_work (start): 0.2509 rms_B_bonded: 2.97 r_work: 0.2354 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8448 Z= 0.112 Angle : 0.623 9.695 11472 Z= 0.292 Chirality : 0.036 0.122 1272 Planarity : 0.005 0.050 1452 Dihedral : 3.009 10.660 1092 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 20.95 % Favored : 76.91 % 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: 3.19 (0.29), residues: 972 helix: 2.75 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 194 TYR 0.015 0.001 TYR H 146 PHE 0.009 0.001 PHE K 114 TRP 0.001 0.000 TRP C 169 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8448) covalent geometry : angle 0.62307 (11472) hydrogen bonds : bond 0.02287 ( 521) hydrogen bonds : angle 3.07235 ( 1515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.221 Fit side-chains REVERT: B 191 ASP cc_start: 0.9202 (t70) cc_final: 0.8812 (t0) REVERT: C 191 ASP cc_start: 0.9229 (t0) cc_final: 0.8826 (t0) REVERT: D 130 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5773 (tt0) REVERT: D 179 GLN cc_start: 0.9196 (tp40) cc_final: 0.8690 (tm-30) REVERT: D 183 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7893 (mt-10) REVERT: D 190 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8472 (mm-30) REVERT: E 147 GLN cc_start: 0.8913 (mt0) cc_final: 0.8522 (mt0) REVERT: E 179 GLN cc_start: 0.8916 (tp40) cc_final: 0.8027 (tp-100) REVERT: F 179 GLN cc_start: 0.8850 (tp40) cc_final: 0.8556 (tm-30) REVERT: G 191 ASP cc_start: 0.9184 (t0) cc_final: 0.8797 (t0) REVERT: H 139 LYS cc_start: 0.9673 (mttm) cc_final: 0.9451 (mttm) REVERT: I 130 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5783 (tt0) REVERT: I 179 GLN cc_start: 0.9096 (tp40) cc_final: 0.8210 (tp-100) REVERT: J 130 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8617 (mm-30) REVERT: J 147 GLN cc_start: 0.8974 (mt0) cc_final: 0.8695 (mt0) REVERT: J 191 ASP cc_start: 0.9170 (t0) cc_final: 0.8761 (t0) REVERT: K 147 GLN cc_start: 0.9023 (mt0) cc_final: 0.8807 (mt0) REVERT: K 179 GLN cc_start: 0.9030 (tp40) cc_final: 0.8632 (tm-30) REVERT: K 183 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: L 191 ASP cc_start: 0.9252 (t0) cc_final: 0.8873 (t0) outliers start: 19 outliers final: 13 residues processed: 251 average time/residue: 0.6182 time to fit residues: 162.2655 Evaluate side-chains 250 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN G 147 GLN H 147 GLN J 179 GLN L 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.057775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.048577 restraints weight = 19461.082| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 2.99 r_work: 0.2331 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8448 Z= 0.116 Angle : 0.608 8.770 11472 Z= 0.289 Chirality : 0.036 0.121 1272 Planarity : 0.005 0.057 1452 Dihedral : 3.007 10.280 1092 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.70 % Allowed : 21.06 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.23 (0.29), residues: 972 helix: 2.77 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 194 TYR 0.015 0.001 TYR H 146 PHE 0.010 0.001 PHE K 114 TRP 0.002 0.000 TRP D 171 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8448) covalent geometry : angle 0.60804 (11472) hydrogen bonds : bond 0.02438 ( 521) hydrogen bonds : angle 3.05725 ( 1515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.222 Fit side-chains REVERT: B 147 GLN cc_start: 0.9148 (mt0) cc_final: 0.8945 (mt0) REVERT: B 191 ASP cc_start: 0.9251 (t70) cc_final: 0.8741 (t0) REVERT: D 130 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5749 (tt0) REVERT: D 179 GLN cc_start: 0.9190 (tp40) cc_final: 0.8652 (tm-30) REVERT: D 183 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7837 (mt-10) REVERT: E 143 ASP cc_start: 0.8478 (t70) cc_final: 0.8250 (t70) REVERT: E 147 GLN cc_start: 0.8934 (mt0) cc_final: 0.8523 (mt0) REVERT: E 179 GLN cc_start: 0.8949 (tp40) cc_final: 0.8064 (tp-100) REVERT: E 194 ARG cc_start: 0.7858 (tmm160) cc_final: 0.7653 (ttp80) REVERT: F 147 GLN cc_start: 0.9192 (mt0) cc_final: 0.8989 (mt0) REVERT: F 179 GLN cc_start: 0.8854 (tp40) cc_final: 0.8388 (tm-30) REVERT: H 139 LYS cc_start: 0.9674 (mttm) cc_final: 0.9455 (mttm) REVERT: I 130 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5841 (tt0) REVERT: I 179 GLN cc_start: 0.9114 (tp40) cc_final: 0.8241 (tp-100) REVERT: I 191 ASP cc_start: 0.9057 (t0) cc_final: 0.8802 (t0) REVERT: J 147 GLN cc_start: 0.9033 (mt0) cc_final: 0.8741 (mt0) REVERT: J 191 ASP cc_start: 0.9190 (t0) cc_final: 0.8866 (t0) REVERT: K 147 GLN cc_start: 0.9065 (mt0) cc_final: 0.8774 (mt0) REVERT: K 179 GLN cc_start: 0.9041 (tp40) cc_final: 0.8675 (tm-30) REVERT: K 183 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: L 179 GLN cc_start: 0.8990 (tp40) cc_final: 0.8369 (tm-30) REVERT: L 191 ASP cc_start: 0.9228 (t0) cc_final: 0.8891 (t0) outliers start: 24 outliers final: 16 residues processed: 250 average time/residue: 0.6014 time to fit residues: 157.2081 Evaluate side-chains 254 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 84 optimal weight: 0.0370 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN G 147 GLN H 147 GLN J 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.059738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.050564 restraints weight = 19470.080| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 2.99 r_work: 0.2378 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8448 Z= 0.114 Angle : 0.625 8.097 11472 Z= 0.298 Chirality : 0.036 0.119 1272 Planarity : 0.005 0.045 1452 Dihedral : 2.869 10.092 1092 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 21.85 % Favored : 76.13 % 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: 3.20 (0.29), residues: 972 helix: 2.74 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.22 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 194 TYR 0.014 0.001 TYR H 146 PHE 0.009 0.001 PHE K 114 TRP 0.001 0.000 TRP E 169 HIS 0.001 0.000 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8448) covalent geometry : angle 0.62506 (11472) hydrogen bonds : bond 0.02086 ( 521) hydrogen bonds : angle 3.03935 ( 1515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.399 Fit side-chains REVERT: B 147 GLN cc_start: 0.9137 (mt0) cc_final: 0.8929 (mt0) REVERT: B 191 ASP cc_start: 0.9184 (t70) cc_final: 0.8816 (t0) REVERT: D 130 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5744 (tt0) REVERT: D 179 GLN cc_start: 0.9207 (tp40) cc_final: 0.8514 (tm-30) REVERT: D 183 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7315 (mt-10) REVERT: E 147 GLN cc_start: 0.8916 (mt0) cc_final: 0.8497 (mt0) REVERT: E 179 GLN cc_start: 0.8955 (tp40) cc_final: 0.8094 (tp-100) REVERT: E 191 ASP cc_start: 0.9076 (t0) cc_final: 0.8724 (t0) REVERT: F 147 GLN cc_start: 0.9153 (mt0) cc_final: 0.8946 (mt0) REVERT: F 179 GLN cc_start: 0.8846 (tp40) cc_final: 0.8397 (tm-30) REVERT: G 194 ARG cc_start: 0.7955 (tmm160) cc_final: 0.7733 (ttp80) REVERT: H 139 LYS cc_start: 0.9668 (mttm) cc_final: 0.9457 (mttm) REVERT: I 130 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5811 (tt0) REVERT: I 179 GLN cc_start: 0.9097 (tp40) cc_final: 0.8229 (tp-100) REVERT: J 147 GLN cc_start: 0.9016 (mt0) cc_final: 0.8721 (mt0) REVERT: J 191 ASP cc_start: 0.9210 (t0) cc_final: 0.8867 (t0) REVERT: K 130 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5816 (tt0) REVERT: K 179 GLN cc_start: 0.9048 (tp40) cc_final: 0.8710 (tm-30) REVERT: K 183 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: L 179 GLN cc_start: 0.9023 (tp40) cc_final: 0.8424 (tm-30) REVERT: L 191 ASP cc_start: 0.9261 (t0) cc_final: 0.8921 (t0) outliers start: 18 outliers final: 12 residues processed: 257 average time/residue: 0.6232 time to fit residues: 167.5598 Evaluate side-chains 252 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 139 LYS Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN E 185 GLN G 147 GLN H 147 GLN H 179 GLN ** I 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN L 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.054582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.046064 restraints weight = 20451.486| |-----------------------------------------------------------------------------| r_work (start): 0.2386 rms_B_bonded: 2.79 r_work: 0.2227 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8448 Z= 0.191 Angle : 0.668 8.524 11472 Z= 0.326 Chirality : 0.039 0.132 1272 Planarity : 0.006 0.084 1452 Dihedral : 3.351 13.029 1092 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.36 % Allowed : 22.30 % Favored : 75.34 % 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: 3.16 (0.29), residues: 972 helix: 2.75 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 194 TYR 0.017 0.001 TYR H 146 PHE 0.010 0.001 PHE K 114 TRP 0.004 0.000 TRP I 171 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8448) covalent geometry : angle 0.66829 (11472) hydrogen bonds : bond 0.03496 ( 521) hydrogen bonds : angle 3.22681 ( 1515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.412 Fit side-chains REVERT: B 191 ASP cc_start: 0.9176 (t70) cc_final: 0.8621 (t0) REVERT: B 194 ARG cc_start: 0.7978 (tmm160) cc_final: 0.7640 (ttp80) REVERT: D 179 GLN cc_start: 0.9047 (tp40) cc_final: 0.8548 (tm-30) REVERT: D 183 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7937 (mt-10) REVERT: D 191 ASP cc_start: 0.8891 (t0) cc_final: 0.8630 (t0) REVERT: E 143 ASP cc_start: 0.8460 (t70) cc_final: 0.8193 (t70) REVERT: E 147 GLN cc_start: 0.8776 (mt0) cc_final: 0.8337 (mt0) REVERT: E 179 GLN cc_start: 0.8804 (tp40) cc_final: 0.7957 (tp-100) REVERT: F 179 GLN cc_start: 0.8731 (tp40) cc_final: 0.8156 (tm-30) REVERT: F 183 GLU cc_start: 0.8647 (tt0) cc_final: 0.8279 (mt-10) REVERT: H 139 LYS cc_start: 0.9631 (mttm) cc_final: 0.9393 (mttm) REVERT: I 130 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5582 (tt0) REVERT: I 179 GLN cc_start: 0.8991 (tp40) cc_final: 0.8145 (tp-100) REVERT: J 191 ASP cc_start: 0.9145 (t0) cc_final: 0.8790 (t0) REVERT: K 179 GLN cc_start: 0.8898 (tp40) cc_final: 0.8524 (tm-30) REVERT: K 183 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: L 179 GLN cc_start: 0.8833 (tp40) cc_final: 0.8286 (tm-30) REVERT: L 191 ASP cc_start: 0.9146 (t0) cc_final: 0.8767 (t0) outliers start: 21 outliers final: 15 residues processed: 244 average time/residue: 0.7857 time to fit residues: 200.1506 Evaluate side-chains 242 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 147 GLN D 185 GLN E 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.056196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.047503 restraints weight = 19858.862| |-----------------------------------------------------------------------------| r_work (start): 0.2446 rms_B_bonded: 2.94 r_work: 0.2290 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 0.003 0.040 8448 Z= 0.129 Angle : 0.678 8.239 11472 Z= 0.325 Chirality : 0.037 0.125 1272 Planarity : 0.005 0.067 1452 Dihedral : 3.121 11.408 1092 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 22.86 % Favored : 75.23 % 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: 3.12 (0.29), residues: 972 helix: 2.72 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.46 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG L 194 TYR 0.013 0.001 TYR H 146 PHE 0.009 0.001 PHE K 114 TRP 0.001 0.000 TRP K 131 HIS 0.002 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8448) covalent geometry : angle 0.67848 (11472) hydrogen bonds : bond 0.02573 ( 521) hydrogen bonds : angle 3.16054 ( 1515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.362 Fit side-chains REVERT: B 191 ASP cc_start: 0.9214 (t70) cc_final: 0.8624 (t0) REVERT: D 179 GLN cc_start: 0.9137 (tp40) cc_final: 0.8615 (tm-30) REVERT: D 183 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7851 (mt-10) REVERT: D 191 ASP cc_start: 0.8955 (t0) cc_final: 0.8562 (t0) REVERT: D 194 ARG cc_start: 0.8086 (tmm160) cc_final: 0.7786 (ttp80) REVERT: E 147 GLN cc_start: 0.8836 (mt0) cc_final: 0.8398 (mt0) REVERT: E 179 GLN cc_start: 0.8866 (tp40) cc_final: 0.8042 (tp-100) REVERT: E 194 ARG cc_start: 0.8006 (tmm160) cc_final: 0.7789 (ttp80) REVERT: F 179 GLN cc_start: 0.8774 (tp40) cc_final: 0.8316 (tm-30) REVERT: G 194 ARG cc_start: 0.8094 (tmm160) cc_final: 0.7764 (ttp80) REVERT: H 139 LYS cc_start: 0.9639 (mttm) cc_final: 0.9405 (mttm) REVERT: I 130 GLU cc_start: 0.5999 (OUTLIER) cc_final: 0.5568 (tt0) REVERT: I 179 GLN cc_start: 0.9037 (tp40) cc_final: 0.8559 (tp-100) REVERT: I 194 ARG cc_start: 0.8039 (tmm160) cc_final: 0.7759 (ttp80) REVERT: J 143 ASP cc_start: 0.8440 (t70) cc_final: 0.8227 (t70) REVERT: J 191 ASP cc_start: 0.9193 (t0) cc_final: 0.8825 (t0) REVERT: K 179 GLN cc_start: 0.8991 (tp40) cc_final: 0.8631 (tm-30) REVERT: K 183 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: K 194 ARG cc_start: 0.8098 (tmm160) cc_final: 0.7769 (ttp80) REVERT: L 179 GLN cc_start: 0.8899 (tp40) cc_final: 0.8187 (tp40) REVERT: L 191 ASP cc_start: 0.9107 (t0) cc_final: 0.8898 (t0) outliers start: 17 outliers final: 12 residues processed: 249 average time/residue: 0.7863 time to fit residues: 204.5514 Evaluate side-chains 244 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 230 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 139 LYS Chi-restraints excluded: chain J residue 186 SER Chi-restraints excluded: chain K residue 164 SER Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain L residue 164 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN G 147 GLN H 147 GLN J 179 GLN K 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.059081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.050299 restraints weight = 19878.667| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 2.82 r_work: 0.2339 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8448 Z= 0.120 Angle : 0.641 8.276 11472 Z= 0.310 Chirality : 0.036 0.121 1272 Planarity : 0.006 0.090 1452 Dihedral : 2.988 13.985 1092 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 23.87 % Favored : 74.89 % 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: 3.09 (0.29), residues: 972 helix: 2.69 (0.20), residues: 804 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG J 194 TYR 0.013 0.001 TYR H 146 PHE 0.009 0.001 PHE K 114 TRP 0.011 0.000 TRP I 131 HIS 0.001 0.000 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8448) covalent geometry : angle 0.64067 (11472) hydrogen bonds : bond 0.02297 ( 521) hydrogen bonds : angle 3.11251 ( 1515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.09 seconds wall clock time: 52 minutes 6.62 seconds (3126.62 seconds total)