Starting phenix.real_space_refine on Thu Feb 5 00:18:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nz5_49951/02_2026/9nz5_49951.map" } resolution = 3.15 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5234 atoms to isotropic. 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 54 5.16 5 C 6179 2.51 5 N 1579 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 9681 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1548 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "D" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1534 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 8, 'TRANS': 183} Chain: "C" Number of atoms: 1694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Conformer: "B" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} bond proxies already assigned to first conformer: 1706 Chain: "B" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Chain: "E" Number of atoms: 1693 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Conformer: "B" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} bond proxies already assigned to first conformer: 1710 Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Time building chain proxies: 2.86, per 1000 atoms: 0.30 Number of scatterers: 9681 At special positions: 0 Unit cell: (61.938, 142.29, 148.986, 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 54 16.00 O 1869 8.00 N 1579 7.00 C 6179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " distance=2.04 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: 0.69 Conformation dependent library (CDL) restraints added in 568.1 milliseconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 24 sheets defined 17.3% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 removed outlier: 3.885A pdb=" N VAL A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 70 removed outlier: 4.856A pdb=" N TRP A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 73 through 105 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.747A pdb=" N ASN A 112 " --> pdb=" O TRP A 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 36 Processing helix chain 'D' and resid 46 through 70 Proline residue: D 58 - end of helix Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.544A pdb=" N SER D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.811A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.086A pdb=" N SER B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.625A pdb=" N LEU E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 193 Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.058A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 131 removed outlier: 7.553A pdb=" N GLU A 166 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 177 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ARG A 199 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS A 179 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG A 197 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 181 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N TYR A 195 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG A 183 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 193 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A 185 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY A 191 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 191 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 126 through 130 removed outlier: 7.258A pdb=" N GLU D 166 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 199 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS D 179 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ARG D 197 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL D 181 " --> pdb=" O TYR D 195 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR D 195 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG D 183 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA D 193 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER D 185 " --> pdb=" O GLY D 191 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY D 191 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.945A pdb=" N PHE C 75 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 74 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 76 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.923A pdb=" N GLU C 109 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 13 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 122 removed outlier: 3.870A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 142 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.614A pdb=" N ALA C 200 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.620A pdb=" N MET B 34 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.586A pdb=" N LYS B 143 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY B 139 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR B 175 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 151 through 154 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.252A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.305A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'E' and resid 133 through 136 Processing sheet with id=AB9, first strand: chain 'E' and resid 149 through 154 removed outlier: 3.987A pdb=" N ALA E 200 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE E 209 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.929A pdb=" N MET F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 50 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 120 through 122 removed outlier: 4.297A pdb=" N LEU F 141 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 120 through 122 removed outlier: 4.297A pdb=" N LEU F 141 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 153 through 154 412 hydrogen bonds defined for protein. 1068 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: 1.46 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2558 1.33 - 1.45: 1944 1.45 - 1.57: 5349 1.57 - 1.69: 0 1.69 - 1.82: 89 Bond restraints: 9940 Sorted by residual: bond pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" C TYR A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.30e-02 5.92e+03 8.00e+00 bond pdb=" N THR E 54 " pdb=" CA THR E 54 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.66e+00 bond pdb=" N THR E 55 " pdb=" CA THR E 55 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 bond pdb=" N TYR E 53 " pdb=" CA TYR E 53 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.91e+00 ... (remaining 9935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 13284 2.55 - 5.11: 235 5.11 - 7.66: 35 7.66 - 10.21: 6 10.21 - 12.76: 5 Bond angle restraints: 13565 Sorted by residual: angle pdb=" CA PHE D 51 " pdb=" CB PHE D 51 " pdb=" CG PHE D 51 " ideal model delta sigma weight residual 113.80 118.32 -4.52 1.00e+00 1.00e+00 2.05e+01 angle pdb=" CA TYR E 53 " pdb=" CB TYR E 53 " pdb=" CG TYR E 53 " ideal model delta sigma weight residual 113.90 121.49 -7.59 1.80e+00 3.09e-01 1.78e+01 angle pdb=" CA TYR C 53 " pdb=" CB TYR C 53 " pdb=" CG TYR C 53 " ideal model delta sigma weight residual 113.90 120.88 -6.98 1.80e+00 3.09e-01 1.50e+01 angle pdb=" CG ARG E 112 " pdb=" CD ARG E 112 " pdb=" NE ARG E 112 " ideal model delta sigma weight residual 112.00 120.31 -8.31 2.20e+00 2.07e-01 1.43e+01 angle pdb=" CA ILE A 200 " pdb=" CB ILE A 200 " pdb=" CG1 ILE A 200 " ideal model delta sigma weight residual 110.40 116.67 -6.27 1.70e+00 3.46e-01 1.36e+01 ... (remaining 13560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4984 17.85 - 35.71: 718 35.71 - 53.56: 178 53.56 - 71.41: 34 71.41 - 89.26: 13 Dihedral angle restraints: 5927 sinusoidal: 2259 harmonic: 3668 Sorted by residual: dihedral pdb=" CB ACYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual -86.00 -164.53 78.53 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB BCYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual -86.00 -164.53 78.53 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS F 140 " pdb=" SG CYS F 140 " pdb=" SG CYS F 195 " pdb=" CB CYS F 195 " ideal model delta sinusoidal sigma weight residual 93.00 42.01 50.99 1 1.00e+01 1.00e-02 3.56e+01 ... (remaining 5924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1346 0.076 - 0.153: 177 0.153 - 0.229: 15 0.229 - 0.305: 2 0.305 - 0.382: 1 Chirality restraints: 1541 Sorted by residual: chirality pdb=" CB ILE B 210 " pdb=" CA ILE B 210 " pdb=" CG1 ILE B 210 " pdb=" CG2 ILE B 210 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CG LEU D 29 " pdb=" CB LEU D 29 " pdb=" CD1 LEU D 29 " pdb=" CD2 LEU D 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE E 154 " pdb=" CA ILE E 154 " pdb=" CG1 ILE E 154 " pdb=" CG2 ILE E 154 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1538 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 117 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO F 118 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO F 118 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO F 118 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 117 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO B 118 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 183 " -0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO F 184 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " -0.037 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 153 2.66 - 3.22: 7948 3.22 - 3.78: 15035 3.78 - 4.34: 19724 4.34 - 4.90: 33797 Nonbonded interactions: 76657 Sorted by model distance: nonbonded pdb=" O THR E 54 " pdb=" OG1 THR E 55 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 106 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASP F 73 " pdb=" OG SER F 75 " model vdw 2.326 3.040 nonbonded pdb=" O THR E 5 " pdb=" OG1 THR E 5 " model vdw 2.336 3.040 nonbonded pdb=" OG SER C 26 " pdb=" OE1 GLN C 27 " model vdw 2.341 3.040 ... (remaining 76652 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' and resid 12 through 203) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 197 or resid 199 through 211 or resid 213 through 218)) \ selection = (chain 'E' and (resid 1 through 19 or resid 21 through 137 or resid 139 through \ 178 or resid 180 through 197 or resid 199 through 211 or resid 213 through 218)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.08 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.930 Find NCS groups from input model: 0.170 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 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 0.060 9948 Z= 0.200 Angle : 0.844 12.764 13584 Z= 0.446 Chirality : 0.052 0.382 1541 Planarity : 0.008 0.123 1704 Dihedral : 17.790 89.264 3552 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.80 % Rotamer: Outliers : 0.18 % Allowed : 33.06 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.18 (0.23), residues: 1243 helix: -1.31 (0.29), residues: 206 sheet: -0.43 (0.25), residues: 463 loop : -2.36 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 112 TYR 0.019 0.002 TYR B 145 PHE 0.023 0.002 PHE D 51 TRP 0.010 0.001 TRP B 188 HIS 0.002 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9940) covalent geometry : angle 0.84419 (13565) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.57607 ( 19) hydrogen bonds : bond 0.16949 ( 384) hydrogen bonds : angle 7.86971 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.321 Fit side-chains REVERT: D 145 ARG cc_start: 0.7116 (mmp80) cc_final: 0.6641 (mmp-170) REVERT: F 135 MET cc_start: 0.6530 (ttm) cc_final: 0.6039 (tmm) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.0745 time to fit residues: 14.6541 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.225235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.163239 restraints weight = 19253.814| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.11 r_work: 0.3489 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9948 Z= 0.131 Angle : 0.566 7.556 13584 Z= 0.295 Chirality : 0.042 0.152 1541 Planarity : 0.006 0.080 1704 Dihedral : 4.620 44.430 1358 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.80 % Favored : 93.12 % Rotamer: Outliers : 2.91 % Allowed : 30.78 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.47 (0.24), residues: 1243 helix: 0.30 (0.35), residues: 209 sheet: -0.27 (0.25), residues: 459 loop : -2.07 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.017 0.001 TYR A 38 PHE 0.010 0.001 PHE D 51 TRP 0.008 0.001 TRP F 154 HIS 0.003 0.001 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9940) covalent geometry : angle 0.56551 (13565) SS BOND : bond 0.00176 ( 8) SS BOND : angle 0.72158 ( 19) hydrogen bonds : bond 0.03767 ( 384) hydrogen bonds : angle 5.70252 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.299 Fit side-chains REVERT: C 97 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: C 171 ASP cc_start: 0.8182 (t0) cc_final: 0.7943 (t0) REVERT: F 135 MET cc_start: 0.6439 (ttm) cc_final: 0.6165 (tmm) outliers start: 32 outliers final: 20 residues processed: 153 average time/residue: 0.0832 time to fit residues: 18.6551 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 203 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 64 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.221987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.158413 restraints weight = 19046.707| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 4.07 r_work: 0.3424 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9948 Z= 0.176 Angle : 0.601 6.746 13584 Z= 0.312 Chirality : 0.043 0.158 1541 Planarity : 0.005 0.065 1704 Dihedral : 4.625 47.616 1358 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 4.55 % Allowed : 29.42 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.22 (0.24), residues: 1243 helix: 0.83 (0.36), residues: 209 sheet: -0.23 (0.25), residues: 458 loop : -1.95 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 112 TYR 0.022 0.002 TYR A 38 PHE 0.012 0.001 PHE B 29 TRP 0.009 0.001 TRP F 154 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9940) covalent geometry : angle 0.60087 (13565) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.77950 ( 19) hydrogen bonds : bond 0.03580 ( 384) hydrogen bonds : angle 5.24320 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.351 Fit side-chains REVERT: A 90 MET cc_start: 0.7277 (mmm) cc_final: 0.6988 (mmt) REVERT: C 97 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: C 171 ASP cc_start: 0.8174 (t0) cc_final: 0.7938 (t0) REVERT: B 209 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6014 (mtpp) REVERT: E 34 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5245 (m-30) REVERT: E 74 ASP cc_start: 0.7727 (t0) cc_final: 0.7512 (t0) REVERT: F 135 MET cc_start: 0.6528 (ttm) cc_final: 0.6125 (tmm) outliers start: 48 outliers final: 28 residues processed: 165 average time/residue: 0.0797 time to fit residues: 19.4351 Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 40.0000 chunk 110 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.220540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156558 restraints weight = 19080.262| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 4.17 r_work: 0.3416 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9948 Z= 0.180 Angle : 0.589 6.968 13584 Z= 0.306 Chirality : 0.043 0.158 1541 Planarity : 0.005 0.055 1704 Dihedral : 4.644 48.602 1358 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 4.55 % Allowed : 28.87 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.14 (0.24), residues: 1243 helix: 1.01 (0.36), residues: 209 sheet: -0.25 (0.25), residues: 458 loop : -1.86 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 112 TYR 0.020 0.002 TYR A 38 PHE 0.011 0.001 PHE D 123 TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9940) covalent geometry : angle 0.58884 (13565) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.71304 ( 19) hydrogen bonds : bond 0.03431 ( 384) hydrogen bonds : angle 5.07625 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7263 (mmm) cc_final: 0.6970 (mmt) REVERT: C 97 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: C 171 ASP cc_start: 0.8217 (t0) cc_final: 0.7975 (t0) REVERT: C 194 ASN cc_start: 0.6089 (OUTLIER) cc_final: 0.5672 (m-40) REVERT: B 209 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6219 (mtpp) REVERT: E 29 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7688 (pt) REVERT: E 34 ASP cc_start: 0.5886 (OUTLIER) cc_final: 0.5089 (t0) REVERT: F 135 MET cc_start: 0.6599 (ttm) cc_final: 0.6177 (tmm) REVERT: F 145 TYR cc_start: 0.7069 (p90) cc_final: 0.6782 (p90) outliers start: 48 outliers final: 34 residues processed: 166 average time/residue: 0.0795 time to fit residues: 19.1064 Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.222216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154326 restraints weight = 17885.170| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.92 r_work: 0.3504 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.118 Angle : 0.547 6.683 13584 Z= 0.281 Chirality : 0.042 0.180 1541 Planarity : 0.005 0.051 1704 Dihedral : 4.455 49.290 1358 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 4.28 % Allowed : 29.23 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.96 (0.25), residues: 1243 helix: 1.24 (0.37), residues: 209 sheet: -0.18 (0.25), residues: 459 loop : -1.75 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 112 TYR 0.014 0.001 TYR A 38 PHE 0.012 0.001 PHE A 123 TRP 0.006 0.001 TRP A 54 HIS 0.002 0.000 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9940) covalent geometry : angle 0.54689 (13565) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.54717 ( 19) hydrogen bonds : bond 0.03051 ( 384) hydrogen bonds : angle 4.86365 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7164 (mmm) cc_final: 0.6892 (mmt) REVERT: C 97 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7067 (mt-10) REVERT: C 171 ASP cc_start: 0.8155 (t0) cc_final: 0.7912 (t0) REVERT: B 209 LYS cc_start: 0.6586 (OUTLIER) cc_final: 0.5993 (mtmm) REVERT: E 6 GLN cc_start: 0.6431 (OUTLIER) cc_final: 0.5562 (pt0) REVERT: E 34 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5423 (t0) REVERT: E 181 SER cc_start: 0.7498 (m) cc_final: 0.7188 (t) REVERT: F 135 MET cc_start: 0.6585 (ttm) cc_final: 0.6173 (tmm) REVERT: F 145 TYR cc_start: 0.7032 (p90) cc_final: 0.6828 (p90) outliers start: 45 outliers final: 33 residues processed: 162 average time/residue: 0.0800 time to fit residues: 19.1136 Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 30.0000 chunk 30 optimal weight: 0.0070 chunk 109 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.222076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.148517 restraints weight = 11118.420| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.02 r_work: 0.3503 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9948 Z= 0.126 Angle : 0.544 6.716 13584 Z= 0.280 Chirality : 0.042 0.163 1541 Planarity : 0.005 0.050 1704 Dihedral : 4.420 49.659 1358 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 4.74 % Allowed : 28.78 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.88 (0.25), residues: 1243 helix: 1.40 (0.37), residues: 207 sheet: -0.18 (0.25), residues: 471 loop : -1.70 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 112 TYR 0.015 0.001 TYR A 38 PHE 0.010 0.001 PHE D 123 TRP 0.007 0.001 TRP E 167 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9940) covalent geometry : angle 0.54428 (13565) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.53990 ( 19) hydrogen bonds : bond 0.03024 ( 384) hydrogen bonds : angle 4.74546 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.7799 (t80) cc_final: 0.7529 (t80) REVERT: A 90 MET cc_start: 0.6946 (mmm) cc_final: 0.6686 (mmt) REVERT: C 97 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: C 171 ASP cc_start: 0.8119 (t0) cc_final: 0.7846 (t0) REVERT: B 209 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5962 (mtmm) REVERT: E 6 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5555 (pt0) REVERT: E 29 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7608 (pt) REVERT: E 181 SER cc_start: 0.7485 (m) cc_final: 0.7179 (t) REVERT: F 60 TYR cc_start: 0.9156 (m-80) cc_final: 0.8684 (m-80) REVERT: F 69 THR cc_start: 0.7339 (OUTLIER) cc_final: 0.7033 (p) REVERT: F 135 MET cc_start: 0.6551 (ttm) cc_final: 0.6142 (tmm) REVERT: F 145 TYR cc_start: 0.6965 (p90) cc_final: 0.6759 (p90) outliers start: 50 outliers final: 38 residues processed: 168 average time/residue: 0.0827 time to fit residues: 20.4545 Evaluate side-chains 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 0.0040 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.223764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166545 restraints weight = 19044.139| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 4.19 r_work: 0.3457 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.108 Angle : 0.538 9.054 13584 Z= 0.273 Chirality : 0.042 0.158 1541 Planarity : 0.005 0.050 1704 Dihedral : 4.320 50.078 1358 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 4.01 % Allowed : 29.14 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.79 (0.25), residues: 1243 helix: 1.47 (0.37), residues: 207 sheet: -0.12 (0.25), residues: 471 loop : -1.65 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.012 0.001 TYR A 38 PHE 0.009 0.001 PHE D 123 TRP 0.007 0.001 TRP E 167 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9940) covalent geometry : angle 0.53770 (13565) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.48884 ( 19) hydrogen bonds : bond 0.02865 ( 384) hydrogen bonds : angle 4.63377 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7187 (mmm) cc_final: 0.6938 (mmt) REVERT: D 130 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7787 (mpt180) REVERT: C 46 GLN cc_start: 0.8849 (mt0) cc_final: 0.8597 (mt0) REVERT: C 97 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: C 171 ASP cc_start: 0.8171 (t0) cc_final: 0.7969 (t0) REVERT: B 209 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5972 (mtmm) REVERT: E 6 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5477 (pt0) REVERT: E 29 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7638 (pt) REVERT: E 34 ASP cc_start: 0.5866 (OUTLIER) cc_final: 0.5580 (t0) REVERT: E 66 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: E 181 SER cc_start: 0.7518 (m) cc_final: 0.7212 (t) REVERT: F 135 MET cc_start: 0.6523 (ttm) cc_final: 0.6113 (tmm) outliers start: 42 outliers final: 32 residues processed: 162 average time/residue: 0.0843 time to fit residues: 19.8347 Evaluate side-chains 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 65 ARG Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.224947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157365 restraints weight = 11124.005| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.03 r_work: 0.3535 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9948 Z= 0.107 Angle : 0.533 7.210 13584 Z= 0.272 Chirality : 0.042 0.165 1541 Planarity : 0.005 0.049 1704 Dihedral : 4.288 51.464 1358 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 4.64 % Allowed : 28.96 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.70 (0.25), residues: 1243 helix: 1.55 (0.37), residues: 207 sheet: -0.06 (0.25), residues: 471 loop : -1.60 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.012 0.001 TYR A 38 PHE 0.010 0.001 PHE D 123 TRP 0.008 0.001 TRP A 54 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9940) covalent geometry : angle 0.53328 (13565) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.47779 ( 19) hydrogen bonds : bond 0.02805 ( 384) hydrogen bonds : angle 4.53010 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6985 (mmm) cc_final: 0.6747 (mmt) REVERT: D 130 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7581 (mpt180) REVERT: C 46 GLN cc_start: 0.8805 (mt0) cc_final: 0.8531 (mt0) REVERT: C 97 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: C 171 ASP cc_start: 0.8099 (t0) cc_final: 0.7866 (t0) REVERT: B 209 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5956 (mtmm) REVERT: E 6 GLN cc_start: 0.6313 (OUTLIER) cc_final: 0.5369 (pt0) REVERT: E 29 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7599 (pt) REVERT: E 74 ASP cc_start: 0.7865 (t0) cc_final: 0.7506 (t0) REVERT: E 181 SER cc_start: 0.7494 (m) cc_final: 0.7183 (t) REVERT: F 60 TYR cc_start: 0.9168 (m-80) cc_final: 0.8586 (m-80) REVERT: F 135 MET cc_start: 0.6519 (ttm) cc_final: 0.6119 (tmm) outliers start: 49 outliers final: 37 residues processed: 167 average time/residue: 0.0827 time to fit residues: 20.4536 Evaluate side-chains 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 203 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.219359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150794 restraints weight = 12851.917| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.18 r_work: 0.3465 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9948 Z= 0.205 Angle : 0.607 6.900 13584 Z= 0.314 Chirality : 0.044 0.189 1541 Planarity : 0.005 0.082 1704 Dihedral : 4.541 50.048 1358 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 4.28 % Allowed : 29.60 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.79 (0.25), residues: 1243 helix: 1.39 (0.37), residues: 206 sheet: -0.18 (0.24), residues: 495 loop : -1.61 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.023 0.002 TYR A 38 PHE 0.012 0.002 PHE D 123 TRP 0.009 0.001 TRP B 154 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 9940) covalent geometry : angle 0.60627 (13565) SS BOND : bond 0.00539 ( 8) SS BOND : angle 0.78788 ( 19) hydrogen bonds : bond 0.03289 ( 384) hydrogen bonds : angle 4.76620 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.7091 (mmm) cc_final: 0.6831 (mmt) REVERT: C 97 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: C 171 ASP cc_start: 0.8127 (t0) cc_final: 0.7876 (t0) REVERT: B 209 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6038 (mtmm) REVERT: E 29 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7626 (pt) REVERT: E 34 ASP cc_start: 0.5897 (OUTLIER) cc_final: 0.5228 (t0) REVERT: E 74 ASP cc_start: 0.7958 (t0) cc_final: 0.7634 (t0) REVERT: F 60 TYR cc_start: 0.9196 (m-80) cc_final: 0.8630 (m-80) REVERT: F 135 MET cc_start: 0.6574 (ttm) cc_final: 0.6154 (tmm) outliers start: 43 outliers final: 34 residues processed: 161 average time/residue: 0.0876 time to fit residues: 20.8497 Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 106 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.223381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152987 restraints weight = 13257.859| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.25 r_work: 0.3527 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9948 Z= 0.110 Angle : 0.546 7.878 13584 Z= 0.281 Chirality : 0.042 0.161 1541 Planarity : 0.005 0.077 1704 Dihedral : 4.385 51.006 1358 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 3.55 % Allowed : 29.96 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.66 (0.25), residues: 1243 helix: 1.60 (0.37), residues: 205 sheet: -0.03 (0.25), residues: 471 loop : -1.58 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.012 0.001 TYR A 38 PHE 0.008 0.001 PHE D 123 TRP 0.008 0.001 TRP E 167 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9940) covalent geometry : angle 0.54622 (13565) SS BOND : bond 0.00147 ( 8) SS BOND : angle 0.54981 ( 19) hydrogen bonds : bond 0.02848 ( 384) hydrogen bonds : angle 4.57845 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6987 (mmm) cc_final: 0.6748 (mmt) REVERT: D 89 MET cc_start: 0.6893 (mtp) cc_final: 0.6201 (tpt) REVERT: D 130 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7584 (mpt180) REVERT: D 134 GLU cc_start: 0.6798 (tp30) cc_final: 0.6597 (tp30) REVERT: D 145 ARG cc_start: 0.7198 (mmp80) cc_final: 0.6752 (mmp-170) REVERT: C 171 ASP cc_start: 0.8118 (t0) cc_final: 0.7869 (t0) REVERT: B 209 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5940 (mtmm) REVERT: E 29 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7549 (pt) REVERT: E 34 ASP cc_start: 0.5943 (OUTLIER) cc_final: 0.5543 (t0) REVERT: E 74 ASP cc_start: 0.7891 (t0) cc_final: 0.7565 (t0) REVERT: E 181 SER cc_start: 0.7498 (m) cc_final: 0.7187 (t) REVERT: F 135 MET cc_start: 0.6559 (ttm) cc_final: 0.6096 (tmm) outliers start: 35 outliers final: 29 residues processed: 155 average time/residue: 0.0824 time to fit residues: 18.9084 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.167126 restraints weight = 19218.764| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 4.09 r_work: 0.3470 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9948 Z= 0.110 Angle : 0.545 8.802 13584 Z= 0.279 Chirality : 0.042 0.163 1541 Planarity : 0.005 0.082 1704 Dihedral : 4.315 50.978 1358 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.47 % Favored : 93.45 % Rotamer: Outliers : 3.64 % Allowed : 29.96 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1243 helix: 1.66 (0.37), residues: 205 sheet: -0.04 (0.25), residues: 493 loop : -1.54 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 112 TYR 0.010 0.001 TYR A 203 PHE 0.009 0.001 PHE D 123 TRP 0.007 0.001 TRP E 167 HIS 0.002 0.000 HIS A 154 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9940) covalent geometry : angle 0.54477 (13565) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.55146 ( 19) hydrogen bonds : bond 0.02812 ( 384) hydrogen bonds : angle 4.48157 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.11 seconds wall clock time: 54 minutes 15.50 seconds (3255.50 seconds total)