Starting phenix.real_space_refine on Wed Sep 17 17:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.cif Found real_map, /net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.map" model { file = "/net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6slq_10239/09_2025/6slq_10239.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6508 2.51 5 N 1800 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1728 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1749 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "F" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1720 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 3.00, per 1000 atoms: 0.29 Number of scatterers: 10336 At special positions: 0 Unit cell: (115.9, 111.02, 84.18, 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 78 16.00 O 1950 8.00 N 1800 7.00 C 6508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=1.53 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.19 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: 0.86 Conformation dependent library (CDL) restraints added in 462.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2476 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 67.0% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.510A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.194A pdb=" N ASN A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.596A pdb=" N LYS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.208A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.586A pdb=" N GLN B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.525A pdb=" N ILE B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.577A pdb=" N LYS B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.955A pdb=" N MET B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.605A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.616A pdb=" N MET C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.627A pdb=" N MET C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.697A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.625A pdb=" N GLN C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 removed outlier: 3.548A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.720A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 173 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.703A pdb=" N TRP D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 220 removed outlier: 3.533A pdb=" N GLY D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.634A pdb=" N MET E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 4.008A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.178A pdb=" N ALA E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.649A pdb=" N GLN E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.188A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.968A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.730A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.546A pdb=" N MET F 66 " --> pdb=" O HIS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.508A pdb=" N GLN F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 174 removed outlier: 3.554A pdb=" N TYR F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 186 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.616A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.716A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.570A pdb=" N VAL A 3 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 11 " --> pdb=" O VAL A 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.465A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.795A pdb=" N VAL D 3 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 11 " --> pdb=" O VAL D 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 3 removed outlier: 4.588A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 577 hydrogen bonds defined for protein. 1731 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: 1.51 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.25: 1780 1.25 - 1.43: 2402 1.43 - 1.60: 6236 1.60 - 1.78: 0 1.78 - 1.95: 148 Bond restraints: 10566 Sorted by residual: bond pdb=" C SER F 146 " pdb=" N PRO F 147 " ideal model delta sigma weight residual 1.335 1.885 -0.550 1.36e-02 5.41e+03 1.63e+03 bond pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 1.335 1.849 -0.514 1.38e-02 5.25e+03 1.39e+03 bond pdb=" C SER E 146 " pdb=" N PRO E 147 " ideal model delta sigma weight residual 1.334 1.952 -0.618 2.34e-02 1.83e+03 6.97e+02 bond pdb=" C SER B 146 " pdb=" N PRO B 147 " ideal model delta sigma weight residual 1.334 1.842 -0.508 2.34e-02 1.83e+03 4.72e+02 bond pdb=" C PRO A 147 " pdb=" N THR A 148 " ideal model delta sigma weight residual 1.331 1.081 0.251 1.38e-02 5.25e+03 3.30e+02 ... (remaining 10561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 14272 3.66 - 7.33: 67 7.33 - 10.99: 11 10.99 - 14.66: 11 14.66 - 18.32: 5 Bond angle restraints: 14366 Sorted by residual: angle pdb=" O SER C 146 " pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 121.31 136.36 -15.05 8.70e-01 1.32e+00 2.99e+02 angle pdb=" CA SER C 146 " pdb=" C SER C 146 " pdb=" N PRO C 147 " ideal model delta sigma weight residual 119.12 103.25 15.87 1.05e+00 9.07e-01 2.28e+02 angle pdb=" O SER F 146 " pdb=" C SER F 146 " pdb=" N PRO F 147 " ideal model delta sigma weight residual 121.31 133.91 -12.60 8.70e-01 1.32e+00 2.10e+02 angle pdb=" C SER C 146 " pdb=" N PRO C 147 " pdb=" CA PRO C 147 " ideal model delta sigma weight residual 119.24 104.23 15.01 1.04e+00 9.25e-01 2.08e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.18 136.81 -14.63 1.08e+00 8.57e-01 1.84e+02 ... (remaining 14361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6210 17.92 - 35.84: 275 35.84 - 53.76: 31 53.76 - 71.68: 2 71.68 - 89.60: 4 Dihedral angle restraints: 6522 sinusoidal: 2704 harmonic: 3818 Sorted by residual: dihedral pdb=" CB CYS C 198 " pdb=" SG CYS C 198 " pdb=" SG CYS C 218 " pdb=" CB CYS C 218 " ideal model delta sinusoidal sigma weight residual -86.00 -13.05 -72.95 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS F 198 " pdb=" SG CYS F 198 " pdb=" SG CYS F 218 " pdb=" CB CYS F 218 " ideal model delta sinusoidal sigma weight residual -86.00 -117.95 31.95 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" C PHE E 32 " pdb=" N PHE E 32 " pdb=" CA PHE E 32 " pdb=" CB PHE E 32 " ideal model delta harmonic sigma weight residual -122.60 -130.68 8.08 0 2.50e+00 1.60e-01 1.04e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1235 0.045 - 0.091: 273 0.091 - 0.136: 74 0.136 - 0.181: 16 0.181 - 0.226: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL F 27 " pdb=" N VAL F 27 " pdb=" C VAL F 27 " pdb=" CB VAL F 27 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LYS C 30 " pdb=" N LYS C 30 " pdb=" C LYS C 30 " pdb=" CB LYS C 30 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1601 not shown) Planarity restraints: 1882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 147 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C PRO E 147 " -0.085 2.00e-02 2.50e+03 pdb=" O PRO E 147 " 0.029 2.00e-02 2.50e+03 pdb=" N THR E 148 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 147 " 0.020 2.00e-02 2.50e+03 4.58e-02 2.09e+01 pdb=" C PRO A 147 " -0.079 2.00e-02 2.50e+03 pdb=" O PRO A 147 " 0.029 2.00e-02 2.50e+03 pdb=" N THR A 148 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 146 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 146 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 146 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 147 " -0.020 2.00e-02 2.50e+03 ... (remaining 1879 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.78: 2015 2.78 - 3.48: 14706 3.48 - 4.19: 22406 4.19 - 4.90: 39280 Nonbonded interactions: 78409 Sorted by model distance: nonbonded pdb=" O THR D 58 " pdb=" OE2 GLU E 35 " model vdw 1.359 3.040 nonbonded pdb=" O PRO F 17 " pdb=" OD1 ASN F 21 " model vdw 2.029 3.040 nonbonded pdb=" O PRO F 17 " pdb=" CG ASN F 21 " model vdw 2.202 3.270 nonbonded pdb=" NZ LYS C 30 " pdb=" OE2 GLU C 35 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU C 71 " pdb=" OG1 THR D 210 " model vdw 2.211 3.040 ... (remaining 78404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.210 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.013 0.618 10572 Z= 0.779 Angle : 0.907 44.170 14378 Z= 0.609 Chirality : 0.045 0.226 1604 Planarity : 0.005 0.070 1882 Dihedral : 9.228 89.602 4028 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.18 % Allowed : 5.04 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -1.02 (0.21), residues: 1310 helix: -0.14 (0.17), residues: 814 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 143 TYR 0.004 0.001 TYR B 130 PHE 0.012 0.001 PHE E 32 TRP 0.003 0.001 TRP F 23 HIS 0.001 0.000 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.01200 (10566) covalent geometry : angle 0.81483 (14366) SS BOND : bond 0.21515 ( 6) SS BOND : angle 13.84623 ( 12) hydrogen bonds : bond 0.13362 ( 577) hydrogen bonds : angle 4.66345 ( 1731) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 604 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7711 (mtp) cc_final: 0.7431 (mtp) REVERT: A 100 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7108 (ttp80) REVERT: A 109 SER cc_start: 0.8397 (m) cc_final: 0.8124 (p) REVERT: A 115 ILE cc_start: 0.8553 (mm) cc_final: 0.8338 (mm) REVERT: A 161 PHE cc_start: 0.8488 (t80) cc_final: 0.8099 (t80) REVERT: A 165 VAL cc_start: 0.9190 (p) cc_final: 0.8658 (p) REVERT: A 214 MET cc_start: 0.8981 (ptp) cc_final: 0.8585 (ppp) REVERT: A 215 MET cc_start: 0.8923 (mtm) cc_final: 0.7896 (mtp) REVERT: B 10 MET cc_start: 0.4214 (mmm) cc_final: 0.3837 (tmm) REVERT: B 30 LYS cc_start: 0.7477 (mttt) cc_final: 0.6371 (mttt) REVERT: B 50 GLN cc_start: 0.8163 (tt0) cc_final: 0.7652 (mt0) REVERT: B 96 MET cc_start: 0.5251 (mmt) cc_final: 0.4086 (mtt) REVERT: B 103 ASP cc_start: 0.8502 (m-30) cc_final: 0.8257 (m-30) REVERT: B 114 GLN cc_start: 0.8283 (pt0) cc_final: 0.7777 (pp30) REVERT: B 131 LYS cc_start: 0.8096 (mtpt) cc_final: 0.7810 (mttt) REVERT: B 134 ILE cc_start: 0.9100 (mt) cc_final: 0.8881 (tp) REVERT: B 141 ILE cc_start: 0.8127 (mt) cc_final: 0.7527 (mt) REVERT: B 190 LEU cc_start: 0.9018 (mt) cc_final: 0.8747 (mt) REVERT: B 214 MET cc_start: 0.8598 (mtt) cc_final: 0.8234 (mmt) REVERT: C 24 VAL cc_start: 0.8228 (t) cc_final: 0.7139 (t) REVERT: C 25 LYS cc_start: 0.8264 (mttt) cc_final: 0.7648 (mtpt) REVERT: C 75 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 98 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8481 (pp20) REVERT: C 100 ARG cc_start: 0.7433 (mmp-170) cc_final: 0.6802 (mtm110) REVERT: C 110 THR cc_start: 0.8097 (t) cc_final: 0.5248 (t) REVERT: C 113 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7033 (mp0) REVERT: C 115 ILE cc_start: 0.9639 (mt) cc_final: 0.9400 (tt) REVERT: C 211 LEU cc_start: 0.8283 (mm) cc_final: 0.7686 (mm) REVERT: D 63 GLN cc_start: 0.7804 (mp10) cc_final: 0.7447 (mp10) REVERT: D 213 GLU cc_start: 0.9185 (pt0) cc_final: 0.8942 (pm20) REVERT: D 215 MET cc_start: 0.8957 (mtm) cc_final: 0.8642 (mtm) REVERT: E 10 MET cc_start: 0.3988 (mmm) cc_final: 0.2448 (tmm) REVERT: E 96 MET cc_start: 0.3569 (mmp) cc_final: 0.2824 (mtt) REVERT: E 98 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6421 (mt-10) REVERT: E 124 ILE cc_start: 0.7377 (mm) cc_final: 0.6823 (mt) REVERT: E 134 ILE cc_start: 0.9165 (mt) cc_final: 0.8826 (tp) REVERT: F 25 LYS cc_start: 0.8750 (mttt) cc_final: 0.8174 (mtpt) REVERT: F 68 MET cc_start: 0.7554 (mtp) cc_final: 0.7181 (mtm) REVERT: F 75 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 100 ARG cc_start: 0.7685 (mmp-170) cc_final: 0.6996 (mtm110) REVERT: F 110 THR cc_start: 0.7649 (t) cc_final: 0.7441 (t) REVERT: F 117 TRP cc_start: 0.8519 (m-10) cc_final: 0.7511 (m-10) REVERT: F 133 TRP cc_start: 0.8221 (m-10) cc_final: 0.7316 (m-10) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.1258 time to fit residues: 99.9352 Evaluate side-chains 363 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** A 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 9 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 179 GLN A 219 GLN B 9 GLN B 95 GLN B 114 GLN B 179 GLN B 193 ASN C 4 GLN C 53 ASN C 84 HIS C 114 GLN C 192 GLN D 4 GLN D 9 GLN D 74 ASN D 87 HIS E 13 GLN E 95 GLN E 114 GLN E 176 GLN E 193 ASN F 4 GLN F 53 ASN F 84 HIS F 192 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.138083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104048 restraints weight = 53229.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109850 restraints weight = 25001.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114207 restraints weight = 14278.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114773 restraints weight = 9455.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116294 restraints weight = 8954.853| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10572 Z= 0.150 Angle : 0.651 7.349 14378 Z= 0.332 Chirality : 0.045 0.238 1604 Planarity : 0.005 0.055 1882 Dihedral : 3.304 22.650 1404 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.44 % Allowed : 2.04 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.24 (0.22), residues: 1310 helix: 0.40 (0.18), residues: 852 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 82 TYR 0.012 0.002 TYR B 164 PHE 0.022 0.002 PHE F 168 TRP 0.026 0.002 TRP D 133 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00343 (10566) covalent geometry : angle 0.64874 (14366) SS BOND : bond 0.00253 ( 6) SS BOND : angle 1.81737 ( 12) hydrogen bonds : bond 0.03812 ( 577) hydrogen bonds : angle 3.79793 ( 1731) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 460 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.8461 (t80) cc_final: 0.8135 (t80) REVERT: A 100 ARG cc_start: 0.7305 (ttt180) cc_final: 0.6887 (ttp80) REVERT: A 131 LYS cc_start: 0.8762 (tttt) cc_final: 0.8541 (tttt) REVERT: A 133 TRP cc_start: 0.8566 (m-10) cc_final: 0.8130 (m-10) REVERT: A 151 LEU cc_start: 0.8802 (tp) cc_final: 0.8565 (mm) REVERT: A 161 PHE cc_start: 0.8485 (t80) cc_final: 0.8106 (t80) REVERT: A 212 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8254 (pt0) REVERT: A 214 MET cc_start: 0.9097 (ptp) cc_final: 0.8654 (ppp) REVERT: A 215 MET cc_start: 0.8761 (mtm) cc_final: 0.8414 (ptm) REVERT: B 50 GLN cc_start: 0.8427 (tt0) cc_final: 0.7430 (mt0) REVERT: B 82 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7772 (ptm160) REVERT: B 96 MET cc_start: 0.5063 (mmt) cc_final: 0.3997 (mtt) REVERT: B 134 ILE cc_start: 0.9211 (mt) cc_final: 0.9002 (tp) REVERT: B 180 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8512 (pm20) REVERT: B 197 ASP cc_start: 0.7205 (p0) cc_final: 0.6876 (p0) REVERT: B 214 MET cc_start: 0.8610 (mtt) cc_final: 0.8070 (mmt) REVERT: C 28 GLU cc_start: 0.7684 (mp0) cc_final: 0.7453 (mt-10) REVERT: C 35 GLU cc_start: 0.9225 (pt0) cc_final: 0.8676 (pt0) REVERT: C 98 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8554 (pp20) REVERT: C 100 ARG cc_start: 0.7655 (mmp-170) cc_final: 0.7069 (mtm110) REVERT: C 110 THR cc_start: 0.8107 (t) cc_final: 0.7872 (m) REVERT: C 131 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8410 (tttp) REVERT: C 133 TRP cc_start: 0.8181 (m-10) cc_final: 0.7711 (m-10) REVERT: C 173 ARG cc_start: 0.8483 (ttp-170) cc_final: 0.8193 (ttp-170) REVERT: D 96 MET cc_start: 0.3058 (mmp) cc_final: 0.2261 (mmt) REVERT: D 213 GLU cc_start: 0.9305 (pt0) cc_final: 0.8911 (pm20) REVERT: D 215 MET cc_start: 0.8450 (mtm) cc_final: 0.7849 (mtt) REVERT: E 10 MET cc_start: 0.3708 (mmm) cc_final: 0.3130 (tmm) REVERT: E 96 MET cc_start: 0.3602 (mmp) cc_final: 0.2679 (mtt) REVERT: E 112 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8590 (tp40) REVERT: E 141 ILE cc_start: 0.8388 (mt) cc_final: 0.8135 (mt) REVERT: E 144 MET cc_start: 0.8080 (ppp) cc_final: 0.7752 (ppp) REVERT: E 161 PHE cc_start: 0.6674 (t80) cc_final: 0.6237 (t80) REVERT: E 214 MET cc_start: 0.9044 (mtm) cc_final: 0.8837 (mtt) REVERT: F 18 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8142 (ttm-80) REVERT: F 25 LYS cc_start: 0.8699 (mttt) cc_final: 0.8455 (tttm) REVERT: F 39 MET cc_start: 0.7568 (tpp) cc_final: 0.7144 (mtt) REVERT: F 104 ILE cc_start: 0.8432 (tt) cc_final: 0.8021 (tp) REVERT: F 110 THR cc_start: 0.8453 (t) cc_final: 0.7807 (t) REVERT: F 133 TRP cc_start: 0.8281 (m-10) cc_final: 0.7422 (m-10) REVERT: F 186 THR cc_start: 0.8820 (p) cc_final: 0.8086 (p) outliers start: 5 outliers final: 0 residues processed: 461 average time/residue: 0.1184 time to fit residues: 72.6411 Evaluate side-chains 328 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 61 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 131 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 GLN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 193 ASN C 179 GLN E 67 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099161 restraints weight = 42934.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103428 restraints weight = 23549.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106360 restraints weight = 15665.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108329 restraints weight = 11767.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109670 restraints weight = 9668.842| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10572 Z= 0.173 Angle : 0.662 8.098 14378 Z= 0.341 Chirality : 0.045 0.190 1604 Planarity : 0.005 0.052 1882 Dihedral : 3.646 19.005 1404 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.18 % Allowed : 3.45 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.07 (0.22), residues: 1310 helix: 0.41 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 82 TYR 0.023 0.002 TYR C 169 PHE 0.017 0.002 PHE F 168 TRP 0.016 0.002 TRP A 133 HIS 0.005 0.001 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00395 (10566) covalent geometry : angle 0.66109 (14366) SS BOND : bond 0.00688 ( 6) SS BOND : angle 1.12700 ( 12) hydrogen bonds : bond 0.03809 ( 577) hydrogen bonds : angle 3.94117 ( 1731) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 418 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 PHE cc_start: 0.8658 (t80) cc_final: 0.8312 (t80) REVERT: A 179 GLN cc_start: 0.8700 (tp40) cc_final: 0.8301 (tp40) REVERT: A 212 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 214 MET cc_start: 0.9043 (ptp) cc_final: 0.8717 (ppp) REVERT: A 215 MET cc_start: 0.8907 (mtm) cc_final: 0.7984 (ptp) REVERT: B 2 ILE cc_start: 0.8875 (tp) cc_final: 0.8673 (tp) REVERT: B 10 MET cc_start: 0.4973 (tmm) cc_final: 0.4330 (tmm) REVERT: B 50 GLN cc_start: 0.8521 (tt0) cc_final: 0.7738 (mt0) REVERT: B 82 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.7797 (ptm160) REVERT: B 115 ILE cc_start: 0.8675 (mt) cc_final: 0.8367 (mt) REVERT: B 118 MET cc_start: 0.8525 (ptt) cc_final: 0.7685 (tpp) REVERT: B 176 GLN cc_start: 0.8281 (mp10) cc_final: 0.8045 (mp10) REVERT: B 197 ASP cc_start: 0.7050 (p0) cc_final: 0.6775 (p0) REVERT: B 214 MET cc_start: 0.8669 (mtt) cc_final: 0.8161 (mmt) REVERT: C 21 ASN cc_start: 0.8196 (m110) cc_final: 0.7790 (m110) REVERT: C 28 GLU cc_start: 0.8206 (mp0) cc_final: 0.7885 (mt-10) REVERT: C 29 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: C 100 ARG cc_start: 0.7879 (mmp-170) cc_final: 0.7162 (mtm110) REVERT: C 131 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8360 (tttt) REVERT: C 173 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.8068 (ttp-170) REVERT: D 55 MET cc_start: 0.9225 (ttt) cc_final: 0.8867 (ttm) REVERT: D 96 MET cc_start: 0.3304 (mmp) cc_final: 0.2925 (mmt) REVERT: D 128 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6419 (tm-30) REVERT: D 131 LYS cc_start: 0.8769 (tttt) cc_final: 0.8473 (tttt) REVERT: D 213 GLU cc_start: 0.9236 (pt0) cc_final: 0.8876 (pm20) REVERT: D 215 MET cc_start: 0.7888 (mtm) cc_final: 0.7667 (ttm) REVERT: E 10 MET cc_start: 0.4037 (mmm) cc_final: 0.3383 (tmm) REVERT: E 96 MET cc_start: 0.4052 (mmp) cc_final: 0.2920 (mtt) REVERT: E 112 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8632 (tp40) REVERT: E 144 MET cc_start: 0.8411 (ppp) cc_final: 0.7596 (ppp) REVERT: E 190 LEU cc_start: 0.9312 (mm) cc_final: 0.9021 (mm) REVERT: E 202 LEU cc_start: 0.8540 (mm) cc_final: 0.8063 (pp) REVERT: E 214 MET cc_start: 0.9148 (mtm) cc_final: 0.8473 (tpt) REVERT: F 25 LYS cc_start: 0.8807 (mttt) cc_final: 0.8588 (tttm) REVERT: F 131 LYS cc_start: 0.8812 (tttt) cc_final: 0.8348 (tttp) outliers start: 2 outliers final: 0 residues processed: 419 average time/residue: 0.1232 time to fit residues: 68.8129 Evaluate side-chains 328 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 127 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 87 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 114 GLN E 179 GLN F 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100335 restraints weight = 46358.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104808 restraints weight = 23972.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107813 restraints weight = 15433.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109762 restraints weight = 11380.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111252 restraints weight = 9253.351| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10572 Z= 0.127 Angle : 0.610 7.754 14378 Z= 0.308 Chirality : 0.044 0.176 1604 Planarity : 0.005 0.053 1882 Dihedral : 3.682 23.061 1404 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.35 % Allowed : 1.68 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.10 (0.22), residues: 1310 helix: 0.54 (0.18), residues: 850 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 154 TYR 0.016 0.002 TYR C 169 PHE 0.018 0.002 PHE B 40 TRP 0.015 0.001 TRP A 133 HIS 0.007 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00296 (10566) covalent geometry : angle 0.60965 (14366) SS BOND : bond 0.00171 ( 6) SS BOND : angle 0.91599 ( 12) hydrogen bonds : bond 0.03482 ( 577) hydrogen bonds : angle 3.79672 ( 1731) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 430 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.5873 (mmm) cc_final: 0.4415 (ttt) REVERT: A 118 MET cc_start: 0.7895 (mtt) cc_final: 0.7614 (mmm) REVERT: A 161 PHE cc_start: 0.8588 (t80) cc_final: 0.8277 (t80) REVERT: A 179 GLN cc_start: 0.8376 (tp40) cc_final: 0.8153 (tp40) REVERT: A 212 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8643 (pt0) REVERT: A 214 MET cc_start: 0.9031 (ptp) cc_final: 0.8768 (ppp) REVERT: A 215 MET cc_start: 0.8495 (mtm) cc_final: 0.8142 (ptp) REVERT: B 10 MET cc_start: 0.5060 (tmm) cc_final: 0.4676 (tmm) REVERT: B 50 GLN cc_start: 0.8526 (tt0) cc_final: 0.7760 (mt0) REVERT: B 63 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8222 (mm-40) REVERT: B 82 ARG cc_start: 0.8111 (ptm-80) cc_final: 0.7823 (ptm160) REVERT: B 115 ILE cc_start: 0.8865 (mt) cc_final: 0.8360 (mt) REVERT: B 118 MET cc_start: 0.8414 (ptt) cc_final: 0.7505 (tpp) REVERT: B 197 ASP cc_start: 0.7040 (p0) cc_final: 0.6776 (p0) REVERT: B 214 MET cc_start: 0.8660 (mtt) cc_final: 0.8374 (mmm) REVERT: C 21 ASN cc_start: 0.8326 (m110) cc_final: 0.7976 (m110) REVERT: C 100 ARG cc_start: 0.7798 (mmp-170) cc_final: 0.7109 (mtm110) REVERT: C 131 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8456 (tttt) REVERT: C 215 MET cc_start: 0.8273 (ttt) cc_final: 0.8043 (ttm) REVERT: D 10 MET cc_start: 0.6791 (mmm) cc_final: 0.4641 (ttt) REVERT: D 40 PHE cc_start: 0.8496 (t80) cc_final: 0.8168 (t80) REVERT: D 55 MET cc_start: 0.9174 (ttt) cc_final: 0.8775 (ttm) REVERT: D 66 MET cc_start: 0.9061 (mmm) cc_final: 0.8788 (mmm) REVERT: D 68 MET cc_start: 0.8273 (mtp) cc_final: 0.7458 (mtt) REVERT: D 96 MET cc_start: 0.2947 (mmp) cc_final: 0.2715 (mmt) REVERT: D 128 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6159 (tm-30) REVERT: D 151 LEU cc_start: 0.8955 (tp) cc_final: 0.8610 (mm) REVERT: D 192 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7952 (tp-100) REVERT: D 212 GLU cc_start: 0.8764 (pt0) cc_final: 0.7946 (pm20) REVERT: D 215 MET cc_start: 0.8101 (mtm) cc_final: 0.7839 (ttm) REVERT: E 10 MET cc_start: 0.4107 (mmm) cc_final: 0.3424 (tmm) REVERT: E 96 MET cc_start: 0.4029 (mmp) cc_final: 0.2887 (mtt) REVERT: E 112 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8616 (tp40) REVERT: E 190 LEU cc_start: 0.9205 (mm) cc_final: 0.8967 (mm) REVERT: E 202 LEU cc_start: 0.8422 (mm) cc_final: 0.8100 (pp) REVERT: E 214 MET cc_start: 0.9149 (mtm) cc_final: 0.8023 (tpt) REVERT: F 18 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8081 (ttm-80) REVERT: F 25 LYS cc_start: 0.8805 (mttt) cc_final: 0.8442 (tptm) REVERT: F 115 ILE cc_start: 0.9670 (mt) cc_final: 0.9364 (tt) REVERT: F 117 TRP cc_start: 0.8123 (m-10) cc_final: 0.7919 (m-10) REVERT: F 131 LYS cc_start: 0.8815 (tttt) cc_final: 0.8440 (tttp) REVERT: F 144 MET cc_start: 0.7178 (tmm) cc_final: 0.5632 (ttp) outliers start: 4 outliers final: 0 residues processed: 430 average time/residue: 0.1034 time to fit residues: 60.5686 Evaluate side-chains 323 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 84 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS F 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.098350 restraints weight = 41313.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102547 restraints weight = 22744.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105383 restraints weight = 15130.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107139 restraints weight = 11363.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108546 restraints weight = 9370.415| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10572 Z= 0.148 Angle : 0.639 6.947 14378 Z= 0.329 Chirality : 0.044 0.147 1604 Planarity : 0.005 0.052 1882 Dihedral : 3.786 20.706 1404 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.18 % Allowed : 2.48 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.04 (0.22), residues: 1310 helix: 0.47 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 173 TYR 0.018 0.002 TYR C 169 PHE 0.014 0.002 PHE D 161 TRP 0.017 0.001 TRP A 133 HIS 0.006 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00339 (10566) covalent geometry : angle 0.63824 (14366) SS BOND : bond 0.00070 ( 6) SS BOND : angle 1.46623 ( 12) hydrogen bonds : bond 0.03521 ( 577) hydrogen bonds : angle 3.95612 ( 1731) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 396 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6127 (mmm) cc_final: 0.4463 (ttt) REVERT: A 23 TRP cc_start: 0.8593 (t-100) cc_final: 0.8271 (t-100) REVERT: A 118 MET cc_start: 0.8036 (mtt) cc_final: 0.7757 (mmm) REVERT: A 161 PHE cc_start: 0.8730 (t80) cc_final: 0.8364 (t80) REVERT: A 179 GLN cc_start: 0.8402 (tp40) cc_final: 0.8100 (tp40) REVERT: A 214 MET cc_start: 0.9031 (ptp) cc_final: 0.8628 (ppp) REVERT: B 10 MET cc_start: 0.4987 (tmm) cc_final: 0.4225 (tmm) REVERT: B 50 GLN cc_start: 0.8445 (tt0) cc_final: 0.7799 (mt0) REVERT: B 63 GLN cc_start: 0.8873 (mm-40) cc_final: 0.7885 (mm-40) REVERT: B 82 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7706 (ptm160) REVERT: B 114 GLN cc_start: 0.8538 (pt0) cc_final: 0.8139 (mp10) REVERT: B 115 ILE cc_start: 0.8896 (mt) cc_final: 0.8680 (mt) REVERT: B 118 MET cc_start: 0.8430 (ptt) cc_final: 0.7687 (tpp) REVERT: B 141 ILE cc_start: 0.8598 (mt) cc_final: 0.8354 (mt) REVERT: B 197 ASP cc_start: 0.6900 (p0) cc_final: 0.6580 (p0) REVERT: B 214 MET cc_start: 0.8627 (mtt) cc_final: 0.8158 (mmp) REVERT: C 18 ARG cc_start: 0.8583 (mtm110) cc_final: 0.7978 (ttm-80) REVERT: C 21 ASN cc_start: 0.8252 (m110) cc_final: 0.7901 (m110) REVERT: C 28 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7240 (mp0) REVERT: C 100 ARG cc_start: 0.7924 (mmp-170) cc_final: 0.7345 (mtm110) REVERT: C 131 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8318 (tttp) REVERT: C 132 ARG cc_start: 0.8401 (ptp-170) cc_final: 0.7733 (ttp-110) REVERT: C 133 TRP cc_start: 0.8017 (m-10) cc_final: 0.6965 (m-10) REVERT: C 143 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7767 (mtt180) REVERT: D 40 PHE cc_start: 0.8632 (t80) cc_final: 0.8306 (t80) REVERT: D 55 MET cc_start: 0.9118 (ttt) cc_final: 0.8707 (ttm) REVERT: D 96 MET cc_start: 0.2934 (mmp) cc_final: 0.2640 (mmt) REVERT: D 128 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6593 (tm-30) REVERT: D 151 LEU cc_start: 0.8890 (tp) cc_final: 0.8582 (mm) REVERT: D 154 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6104 (mtm-85) REVERT: D 167 ARG cc_start: 0.8900 (ptm160) cc_final: 0.8665 (ptm160) REVERT: D 215 MET cc_start: 0.8106 (mtm) cc_final: 0.7834 (ttm) REVERT: E 10 MET cc_start: 0.4288 (mmm) cc_final: 0.3587 (tmm) REVERT: E 68 MET cc_start: 0.8009 (mtp) cc_final: 0.7769 (mtp) REVERT: E 190 LEU cc_start: 0.9260 (mm) cc_final: 0.9005 (mm) REVERT: E 202 LEU cc_start: 0.8489 (mm) cc_final: 0.8079 (pp) REVERT: E 214 MET cc_start: 0.9195 (mtm) cc_final: 0.8285 (tpt) REVERT: F 25 LYS cc_start: 0.8835 (mttt) cc_final: 0.8415 (tptm) REVERT: F 131 LYS cc_start: 0.8918 (tttt) cc_final: 0.8488 (tttp) REVERT: F 144 MET cc_start: 0.6500 (tmm) cc_final: 0.6037 (ttt) outliers start: 2 outliers final: 0 residues processed: 397 average time/residue: 0.1133 time to fit residues: 60.5537 Evaluate side-chains 311 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN D 84 HIS D 87 HIS ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091378 restraints weight = 57797.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095980 restraints weight = 28216.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.099192 restraints weight = 17660.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101449 restraints weight = 12688.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103049 restraints weight = 10055.882| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10572 Z= 0.213 Angle : 0.717 7.685 14378 Z= 0.376 Chirality : 0.047 0.205 1604 Planarity : 0.006 0.054 1882 Dihedral : 4.272 19.900 1404 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.35 % Allowed : 2.39 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1310 helix: 0.25 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -0.63 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 100 TYR 0.024 0.003 TYR C 169 PHE 0.017 0.002 PHE C 168 TRP 0.021 0.002 TRP A 117 HIS 0.010 0.002 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00472 (10566) covalent geometry : angle 0.71567 (14366) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.52881 ( 12) hydrogen bonds : bond 0.04113 ( 577) hydrogen bonds : angle 4.24452 ( 1731) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 388 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.8717 (t-100) cc_final: 0.8464 (t-100) REVERT: A 113 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8767 (mt-10) REVERT: A 118 MET cc_start: 0.8124 (mtt) cc_final: 0.7809 (mmm) REVERT: A 131 LYS cc_start: 0.8639 (tttt) cc_final: 0.8410 (tptm) REVERT: A 154 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6515 (mtm-85) REVERT: A 161 PHE cc_start: 0.8699 (t80) cc_final: 0.8289 (t80) REVERT: A 214 MET cc_start: 0.8968 (ptp) cc_final: 0.8651 (ppp) REVERT: A 215 MET cc_start: 0.8137 (ptp) cc_final: 0.7738 (ptp) REVERT: B 10 MET cc_start: 0.5379 (tmm) cc_final: 0.4699 (tmm) REVERT: B 50 GLN cc_start: 0.8525 (tt0) cc_final: 0.7325 (mt0) REVERT: B 82 ARG cc_start: 0.7955 (ptm-80) cc_final: 0.7650 (ptm160) REVERT: B 124 ILE cc_start: 0.7255 (mm) cc_final: 0.6995 (mm) REVERT: B 141 ILE cc_start: 0.8705 (mt) cc_final: 0.8439 (mt) REVERT: B 143 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: B 144 MET cc_start: 0.8346 (ppp) cc_final: 0.7979 (ppp) REVERT: B 197 ASP cc_start: 0.7010 (p0) cc_final: 0.6687 (p0) REVERT: C 18 ARG cc_start: 0.8560 (mtm110) cc_final: 0.8354 (ttm110) REVERT: C 21 ASN cc_start: 0.8286 (m110) cc_final: 0.7992 (t0) REVERT: C 28 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7860 (mt-10) REVERT: C 29 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: C 100 ARG cc_start: 0.8138 (mmp-170) cc_final: 0.7453 (mtm110) REVERT: C 131 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8227 (tttt) REVERT: C 132 ARG cc_start: 0.8367 (ptp-170) cc_final: 0.7769 (ttp-110) REVERT: C 133 TRP cc_start: 0.8111 (m-10) cc_final: 0.7195 (m-10) REVERT: C 214 MET cc_start: 0.8826 (mtt) cc_final: 0.8520 (mtt) REVERT: D 10 MET cc_start: 0.6567 (mmm) cc_final: 0.5515 (ttt) REVERT: D 55 MET cc_start: 0.9103 (ttt) cc_final: 0.8711 (ttm) REVERT: D 66 MET cc_start: 0.9106 (mmm) cc_final: 0.8819 (mmm) REVERT: D 114 GLN cc_start: 0.9246 (pt0) cc_final: 0.8937 (pt0) REVERT: D 118 MET cc_start: 0.8362 (mtt) cc_final: 0.8099 (mmm) REVERT: D 128 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6427 (tm-30) REVERT: D 131 LYS cc_start: 0.8425 (tttt) cc_final: 0.8002 (tptm) REVERT: D 133 TRP cc_start: 0.8538 (m-10) cc_final: 0.8124 (m-10) REVERT: D 154 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.6632 (mtm-85) REVERT: D 212 GLU cc_start: 0.8807 (pt0) cc_final: 0.8078 (pm20) REVERT: E 10 MET cc_start: 0.4529 (mmm) cc_final: 0.3837 (tmm) REVERT: E 68 MET cc_start: 0.8048 (mtp) cc_final: 0.7754 (ttm) REVERT: E 98 GLU cc_start: 0.8251 (tp30) cc_final: 0.7990 (tp30) REVERT: E 190 LEU cc_start: 0.9391 (mm) cc_final: 0.9063 (mm) REVERT: E 202 LEU cc_start: 0.8592 (mm) cc_final: 0.8382 (mm) REVERT: E 214 MET cc_start: 0.9087 (mtm) cc_final: 0.8869 (mtp) REVERT: F 18 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8105 (ttm-80) REVERT: F 25 LYS cc_start: 0.8786 (mttt) cc_final: 0.8464 (tptm) REVERT: F 100 ARG cc_start: 0.8675 (mtp-110) cc_final: 0.8473 (mtm110) REVERT: F 131 LYS cc_start: 0.8853 (tttt) cc_final: 0.8188 (tptt) REVERT: F 139 ASN cc_start: 0.9487 (m-40) cc_final: 0.9080 (m110) REVERT: F 144 MET cc_start: 0.6169 (tmm) cc_final: 0.5551 (ttp) outliers start: 4 outliers final: 0 residues processed: 389 average time/residue: 0.1158 time to fit residues: 60.3173 Evaluate side-chains 303 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 34 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 70 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN E 67 GLN E 84 HIS F 74 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091386 restraints weight = 46318.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.095598 restraints weight = 24258.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098503 restraints weight = 15728.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100505 restraints weight = 11615.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101902 restraints weight = 9395.023| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10572 Z= 0.184 Angle : 0.692 7.726 14378 Z= 0.361 Chirality : 0.046 0.136 1604 Planarity : 0.005 0.054 1882 Dihedral : 4.269 20.813 1404 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.13 (0.22), residues: 1310 helix: 0.29 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -0.62 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 154 TYR 0.023 0.002 TYR C 169 PHE 0.013 0.002 PHE A 32 TRP 0.016 0.002 TRP A 23 HIS 0.007 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00421 (10566) covalent geometry : angle 0.69126 (14366) SS BOND : bond 0.00145 ( 6) SS BOND : angle 1.31055 ( 12) hydrogen bonds : bond 0.03982 ( 577) hydrogen bonds : angle 4.30184 ( 1731) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6869 (mmm) cc_final: 0.5831 (ttt) REVERT: A 113 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8693 (mt-10) REVERT: A 118 MET cc_start: 0.8241 (mtt) cc_final: 0.7956 (mmm) REVERT: A 154 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.5948 (mtm-85) REVERT: A 161 PHE cc_start: 0.8704 (t80) cc_final: 0.8320 (t80) REVERT: A 203 LYS cc_start: 0.8927 (mttt) cc_final: 0.8686 (mtmm) REVERT: A 214 MET cc_start: 0.9019 (ptp) cc_final: 0.8691 (ppp) REVERT: A 215 MET cc_start: 0.8297 (ptp) cc_final: 0.7973 (ptp) REVERT: B 10 MET cc_start: 0.5358 (tmm) cc_final: 0.4683 (tmm) REVERT: B 50 GLN cc_start: 0.8520 (tt0) cc_final: 0.7133 (mt0) REVERT: B 82 ARG cc_start: 0.7797 (ptm-80) cc_final: 0.7517 (ptm160) REVERT: B 118 MET cc_start: 0.8488 (ptt) cc_final: 0.7411 (tpp) REVERT: B 143 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7485 (ttm-80) REVERT: B 197 ASP cc_start: 0.7039 (p0) cc_final: 0.6714 (p0) REVERT: B 214 MET cc_start: 0.8832 (mmm) cc_final: 0.8065 (mmp) REVERT: C 25 LYS cc_start: 0.8338 (ttpt) cc_final: 0.7531 (ttpt) REVERT: C 28 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7434 (mp0) REVERT: C 100 ARG cc_start: 0.8186 (mmp-170) cc_final: 0.7581 (mtm110) REVERT: C 131 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8291 (tttt) REVERT: C 132 ARG cc_start: 0.8382 (ptp-170) cc_final: 0.7707 (ttp-110) REVERT: C 133 TRP cc_start: 0.8038 (m-10) cc_final: 0.6983 (m-10) REVERT: C 143 ARG cc_start: 0.8141 (mtt180) cc_final: 0.7870 (ttm170) REVERT: C 214 MET cc_start: 0.8813 (mtt) cc_final: 0.8415 (mtt) REVERT: D 10 MET cc_start: 0.6924 (mmm) cc_final: 0.5799 (ttt) REVERT: D 48 THR cc_start: 0.9073 (p) cc_final: 0.8170 (p) REVERT: D 55 MET cc_start: 0.9108 (ttt) cc_final: 0.8724 (ttm) REVERT: D 66 MET cc_start: 0.9138 (mmm) cc_final: 0.8923 (mmm) REVERT: D 118 MET cc_start: 0.8363 (mtt) cc_final: 0.8069 (mmm) REVERT: D 128 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6227 (tm-30) REVERT: D 154 ARG cc_start: 0.7254 (mtm-85) cc_final: 0.6616 (mtm-85) REVERT: D 167 ARG cc_start: 0.8966 (ptm160) cc_final: 0.8684 (ptm-80) REVERT: D 189 LEU cc_start: 0.9412 (mm) cc_final: 0.9195 (mm) REVERT: D 212 GLU cc_start: 0.8808 (pt0) cc_final: 0.8041 (pm20) REVERT: D 215 MET cc_start: 0.8739 (ttp) cc_final: 0.8511 (ttm) REVERT: E 10 MET cc_start: 0.4580 (mmm) cc_final: 0.3882 (tmm) REVERT: E 68 MET cc_start: 0.8122 (mtp) cc_final: 0.7894 (ttm) REVERT: E 214 MET cc_start: 0.9168 (mtm) cc_final: 0.8932 (mtp) REVERT: F 21 ASN cc_start: 0.8200 (m110) cc_final: 0.7883 (m110) REVERT: F 25 LYS cc_start: 0.8673 (mttt) cc_final: 0.8184 (tptm) REVERT: F 100 ARG cc_start: 0.8700 (mtp-110) cc_final: 0.8490 (mtm110) REVERT: F 131 LYS cc_start: 0.8802 (tttt) cc_final: 0.8195 (tptt) REVERT: F 144 MET cc_start: 0.6167 (tmm) cc_final: 0.5551 (ttp) REVERT: F 164 TYR cc_start: 0.8810 (t80) cc_final: 0.7735 (t80) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1199 time to fit residues: 61.3507 Evaluate side-chains 300 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 92 optimal weight: 9.9990 chunk 58 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 HIS D 87 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.124459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090149 restraints weight = 60689.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094760 restraints weight = 28638.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.097863 restraints weight = 17690.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100059 restraints weight = 12700.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101593 restraints weight = 10052.185| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10572 Z= 0.172 Angle : 0.680 6.966 14378 Z= 0.354 Chirality : 0.046 0.143 1604 Planarity : 0.005 0.052 1882 Dihedral : 4.349 19.662 1404 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.18 % Allowed : 1.86 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.09 (0.22), residues: 1310 helix: 0.29 (0.17), residues: 866 sheet: None (None), residues: 0 loop : -0.54 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 18 TYR 0.020 0.003 TYR C 169 PHE 0.015 0.002 PHE B 32 TRP 0.018 0.001 TRP A 117 HIS 0.005 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00390 (10566) covalent geometry : angle 0.67918 (14366) SS BOND : bond 0.00146 ( 6) SS BOND : angle 1.32768 ( 12) hydrogen bonds : bond 0.03879 ( 577) hydrogen bonds : angle 4.29641 ( 1731) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6875 (mmm) cc_final: 0.5853 (ttt) REVERT: A 118 MET cc_start: 0.8232 (mtt) cc_final: 0.7973 (mmm) REVERT: A 161 PHE cc_start: 0.8662 (t80) cc_final: 0.8276 (t80) REVERT: A 203 LYS cc_start: 0.8972 (mttt) cc_final: 0.8712 (mtmm) REVERT: A 214 MET cc_start: 0.9069 (ptp) cc_final: 0.8711 (ppp) REVERT: A 215 MET cc_start: 0.8316 (ptp) cc_final: 0.7879 (ptm) REVERT: B 10 MET cc_start: 0.5080 (tmm) cc_final: 0.4433 (tmm) REVERT: B 50 GLN cc_start: 0.8557 (tt0) cc_final: 0.7232 (mt0) REVERT: B 82 ARG cc_start: 0.7806 (ptm-80) cc_final: 0.7545 (ptm160) REVERT: B 141 ILE cc_start: 0.8755 (mt) cc_final: 0.8479 (mt) REVERT: B 144 MET cc_start: 0.8009 (ppp) cc_final: 0.7495 (ppp) REVERT: B 197 ASP cc_start: 0.7054 (p0) cc_final: 0.6767 (p0) REVERT: C 39 MET cc_start: 0.8055 (mtt) cc_final: 0.7767 (tpp) REVERT: C 73 ILE cc_start: 0.8707 (mm) cc_final: 0.8383 (mt) REVERT: C 100 ARG cc_start: 0.8281 (mmp-170) cc_final: 0.7642 (mtm110) REVERT: C 131 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8283 (tttt) REVERT: C 132 ARG cc_start: 0.8397 (ptp-170) cc_final: 0.7693 (ttp-110) REVERT: C 133 TRP cc_start: 0.8166 (m-10) cc_final: 0.7159 (m-10) REVERT: C 143 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7524 (tpt90) REVERT: C 144 MET cc_start: 0.6153 (tmm) cc_final: 0.5477 (ttp) REVERT: C 189 LEU cc_start: 0.9058 (mm) cc_final: 0.8854 (mm) REVERT: C 214 MET cc_start: 0.8765 (mtt) cc_final: 0.8465 (mtt) REVERT: D 10 MET cc_start: 0.7200 (mmm) cc_final: 0.6361 (ttt) REVERT: D 48 THR cc_start: 0.9034 (p) cc_final: 0.8125 (p) REVERT: D 55 MET cc_start: 0.9032 (ttt) cc_final: 0.8672 (ttm) REVERT: D 66 MET cc_start: 0.9117 (mmm) cc_final: 0.8836 (mmm) REVERT: D 118 MET cc_start: 0.8316 (mtt) cc_final: 0.8054 (mmm) REVERT: D 128 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6373 (tm-30) REVERT: D 151 LEU cc_start: 0.8269 (tp) cc_final: 0.7765 (mm) REVERT: D 154 ARG cc_start: 0.7288 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: D 167 ARG cc_start: 0.8946 (ptm160) cc_final: 0.8634 (ptm160) REVERT: E 10 MET cc_start: 0.4609 (mmm) cc_final: 0.3907 (tmm) REVERT: E 68 MET cc_start: 0.8038 (mtp) cc_final: 0.7689 (ttm) REVERT: F 18 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.8159 (ttp80) REVERT: F 21 ASN cc_start: 0.8074 (m110) cc_final: 0.7712 (m110) REVERT: F 25 LYS cc_start: 0.8703 (mttt) cc_final: 0.8259 (tptp) REVERT: F 131 LYS cc_start: 0.8804 (tttt) cc_final: 0.8213 (tptt) REVERT: F 164 TYR cc_start: 0.8849 (t80) cc_final: 0.7807 (t80) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.1129 time to fit residues: 57.7883 Evaluate side-chains 292 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 25 optimal weight: 0.0470 chunk 123 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094999 restraints weight = 36195.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098746 restraints weight = 20419.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101334 restraints weight = 13780.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102975 restraints weight = 10452.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.104286 restraints weight = 8684.344| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10572 Z= 0.131 Angle : 0.671 8.658 14378 Z= 0.343 Chirality : 0.045 0.139 1604 Planarity : 0.005 0.062 1882 Dihedral : 4.265 21.939 1404 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.09 % Allowed : 0.62 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.04 (0.22), residues: 1310 helix: 0.41 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -0.50 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 18 TYR 0.019 0.002 TYR B 164 PHE 0.013 0.002 PHE E 161 TRP 0.016 0.001 TRP E 23 HIS 0.003 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00304 (10566) covalent geometry : angle 0.66975 (14366) SS BOND : bond 0.00262 ( 6) SS BOND : angle 1.64556 ( 12) hydrogen bonds : bond 0.03696 ( 577) hydrogen bonds : angle 4.16435 ( 1731) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6799 (mmm) cc_final: 0.5756 (ttm) REVERT: A 113 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8756 (mt-10) REVERT: A 118 MET cc_start: 0.8162 (mtt) cc_final: 0.7892 (mmm) REVERT: A 154 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7456 (mtm-85) REVERT: A 203 LYS cc_start: 0.8937 (mttt) cc_final: 0.8658 (mtmm) REVERT: A 214 MET cc_start: 0.9048 (ptp) cc_final: 0.8695 (ppp) REVERT: A 215 MET cc_start: 0.8360 (ptp) cc_final: 0.8115 (ptp) REVERT: B 10 MET cc_start: 0.5013 (tmm) cc_final: 0.4381 (tmm) REVERT: B 50 GLN cc_start: 0.8430 (tt0) cc_final: 0.7282 (mt0) REVERT: B 82 ARG cc_start: 0.7811 (ptm-80) cc_final: 0.7540 (ptm160) REVERT: B 114 GLN cc_start: 0.8576 (pt0) cc_final: 0.7560 (mt0) REVERT: B 118 MET cc_start: 0.7938 (ptp) cc_final: 0.7465 (tpt) REVERT: B 141 ILE cc_start: 0.8845 (mt) cc_final: 0.8533 (mt) REVERT: B 197 ASP cc_start: 0.6973 (p0) cc_final: 0.6659 (p0) REVERT: C 39 MET cc_start: 0.8006 (mtt) cc_final: 0.7725 (tpp) REVERT: C 73 ILE cc_start: 0.8655 (mm) cc_final: 0.8359 (mt) REVERT: C 100 ARG cc_start: 0.8159 (mmp-170) cc_final: 0.7519 (mtm110) REVERT: C 131 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8285 (tttt) REVERT: C 132 ARG cc_start: 0.8262 (ptp-170) cc_final: 0.7801 (ttp-110) REVERT: C 133 TRP cc_start: 0.8015 (m-10) cc_final: 0.7036 (m-10) REVERT: C 193 ASN cc_start: 0.7172 (m-40) cc_final: 0.6259 (t0) REVERT: C 214 MET cc_start: 0.8663 (mtt) cc_final: 0.8114 (mtt) REVERT: D 10 MET cc_start: 0.7114 (mmm) cc_final: 0.6184 (ttt) REVERT: D 48 THR cc_start: 0.9069 (p) cc_final: 0.8091 (p) REVERT: D 55 MET cc_start: 0.8971 (ttt) cc_final: 0.8674 (ttm) REVERT: D 66 MET cc_start: 0.9072 (mmm) cc_final: 0.8762 (mmm) REVERT: D 70 LYS cc_start: 0.8682 (tttt) cc_final: 0.8430 (tttp) REVERT: D 128 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6537 (tm-30) REVERT: D 131 LYS cc_start: 0.8326 (tttt) cc_final: 0.8115 (tptm) REVERT: D 154 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6492 (mtm-85) REVERT: D 167 ARG cc_start: 0.8971 (ptm160) cc_final: 0.8712 (ptm160) REVERT: D 189 LEU cc_start: 0.9446 (mm) cc_final: 0.9223 (mm) REVERT: E 10 MET cc_start: 0.4417 (mmm) cc_final: 0.3602 (tmm) REVERT: E 115 ILE cc_start: 0.8952 (mt) cc_final: 0.8646 (mt) REVERT: E 118 MET cc_start: 0.8565 (ptt) cc_final: 0.7603 (tpp) REVERT: F 21 ASN cc_start: 0.8122 (m110) cc_final: 0.7693 (m110) REVERT: F 25 LYS cc_start: 0.8443 (mttt) cc_final: 0.7980 (ttpt) REVERT: F 28 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7195 (mp0) REVERT: F 66 MET cc_start: 0.8341 (mpp) cc_final: 0.7755 (ttm) REVERT: F 129 ILE cc_start: 0.8626 (pt) cc_final: 0.8385 (pt) REVERT: F 131 LYS cc_start: 0.8782 (tttt) cc_final: 0.8240 (tptt) REVERT: F 144 MET cc_start: 0.6912 (tmm) cc_final: 0.6249 (ttp) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.1130 time to fit residues: 59.3986 Evaluate side-chains 307 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 0.0060 chunk 56 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 HIS D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN F 74 ASN F 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.096403 restraints weight = 51776.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101029 restraints weight = 25737.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104061 restraints weight = 16190.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106221 restraints weight = 11774.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107658 restraints weight = 9395.989| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10572 Z= 0.127 Angle : 0.674 8.189 14378 Z= 0.339 Chirality : 0.045 0.146 1604 Planarity : 0.005 0.060 1882 Dihedral : 4.130 19.043 1404 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.18 % Allowed : 0.35 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.13 (0.23), residues: 1310 helix: 0.46 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -0.43 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.021 0.002 TYR C 145 PHE 0.021 0.002 PHE A 32 TRP 0.018 0.001 TRP B 23 HIS 0.005 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00282 (10566) covalent geometry : angle 0.67258 (14366) SS BOND : bond 0.00272 ( 6) SS BOND : angle 1.54576 ( 12) hydrogen bonds : bond 0.03430 ( 577) hydrogen bonds : angle 4.11911 ( 1731) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 404 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.6756 (mmm) cc_final: 0.5713 (ttt) REVERT: A 40 PHE cc_start: 0.8767 (t80) cc_final: 0.8455 (t80) REVERT: A 118 MET cc_start: 0.8171 (mtt) cc_final: 0.7947 (mmm) REVERT: A 161 PHE cc_start: 0.8568 (t80) cc_final: 0.8295 (t80) REVERT: A 203 LYS cc_start: 0.8927 (mttt) cc_final: 0.8672 (mtmm) REVERT: A 214 MET cc_start: 0.9054 (ptp) cc_final: 0.8664 (ppp) REVERT: A 215 MET cc_start: 0.8299 (ptp) cc_final: 0.8005 (ptp) REVERT: B 10 MET cc_start: 0.5009 (tmm) cc_final: 0.4262 (tmm) REVERT: B 16 SER cc_start: 0.8691 (m) cc_final: 0.8372 (p) REVERT: B 50 GLN cc_start: 0.8425 (tt0) cc_final: 0.7267 (mt0) REVERT: B 68 MET cc_start: 0.7842 (ttm) cc_final: 0.7399 (ttm) REVERT: B 82 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.7662 (ptm160) REVERT: B 114 GLN cc_start: 0.8454 (pt0) cc_final: 0.7192 (mt0) REVERT: B 118 MET cc_start: 0.7898 (ptp) cc_final: 0.7610 (tpt) REVERT: B 141 ILE cc_start: 0.8774 (mt) cc_final: 0.8460 (mt) REVERT: B 197 ASP cc_start: 0.6904 (p0) cc_final: 0.6574 (p0) REVERT: C 18 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8417 (ttm-80) REVERT: C 100 ARG cc_start: 0.8086 (mmp-170) cc_final: 0.7322 (mtm110) REVERT: C 131 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8168 (tttp) REVERT: C 132 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7701 (ttp-110) REVERT: C 133 TRP cc_start: 0.7844 (m-10) cc_final: 0.7135 (m-10) REVERT: C 144 MET cc_start: 0.5804 (tmm) cc_final: 0.4911 (ttp) REVERT: C 193 ASN cc_start: 0.7054 (m-40) cc_final: 0.6819 (t0) REVERT: C 214 MET cc_start: 0.8411 (mtt) cc_final: 0.8108 (mtt) REVERT: D 10 MET cc_start: 0.7000 (mmm) cc_final: 0.6039 (ttm) REVERT: D 48 THR cc_start: 0.8964 (p) cc_final: 0.8128 (p) REVERT: D 55 MET cc_start: 0.8914 (ttt) cc_final: 0.8613 (ttm) REVERT: D 66 MET cc_start: 0.9078 (mmm) cc_final: 0.8711 (mmm) REVERT: D 128 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6100 (tm-30) REVERT: D 132 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7900 (ttm110) REVERT: D 151 LEU cc_start: 0.8596 (tp) cc_final: 0.8141 (mm) REVERT: D 167 ARG cc_start: 0.9027 (ptm160) cc_final: 0.8766 (ptm160) REVERT: D 212 GLU cc_start: 0.8782 (pt0) cc_final: 0.7959 (pm20) REVERT: E 10 MET cc_start: 0.4348 (mmm) cc_final: 0.3563 (tmm) REVERT: E 63 GLN cc_start: 0.8816 (mm-40) cc_final: 0.7913 (mm-40) REVERT: E 72 THR cc_start: 0.8926 (p) cc_final: 0.8717 (p) REVERT: E 115 ILE cc_start: 0.8905 (mt) cc_final: 0.8616 (mt) REVERT: E 118 MET cc_start: 0.8340 (ptt) cc_final: 0.7690 (tpt) REVERT: E 190 LEU cc_start: 0.9312 (mm) cc_final: 0.8955 (mm) REVERT: E 202 LEU cc_start: 0.8611 (mm) cc_final: 0.8138 (pp) REVERT: F 21 ASN cc_start: 0.7991 (m110) cc_final: 0.7668 (m110) REVERT: F 25 LYS cc_start: 0.8565 (mttt) cc_final: 0.7984 (tptp) REVERT: F 28 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7091 (mp0) REVERT: F 63 GLN cc_start: 0.8858 (mp10) cc_final: 0.8642 (mp10) REVERT: F 66 MET cc_start: 0.8327 (mpp) cc_final: 0.7756 (ttm) REVERT: F 129 ILE cc_start: 0.8580 (pt) cc_final: 0.8345 (pt) REVERT: F 131 LYS cc_start: 0.8752 (tttt) cc_final: 0.8200 (tptt) REVERT: F 144 MET cc_start: 0.6873 (tmm) cc_final: 0.6182 (ttp) outliers start: 2 outliers final: 1 residues processed: 405 average time/residue: 0.1198 time to fit residues: 65.3350 Evaluate side-chains 326 residues out of total 1126 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 99 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 overall best weight: 2.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.094024 restraints weight = 58532.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098715 restraints weight = 28395.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101887 restraints weight = 17628.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.104066 restraints weight = 12650.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.105586 restraints weight = 10047.995| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.7092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10572 Z= 0.144 Angle : 0.706 10.707 14378 Z= 0.362 Chirality : 0.046 0.143 1604 Planarity : 0.005 0.061 1882 Dihedral : 4.242 18.835 1404 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 0.13 (0.23), residues: 1310 helix: 0.44 (0.18), residues: 848 sheet: None (None), residues: 0 loop : -0.37 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.021 0.002 TYR B 164 PHE 0.014 0.002 PHE F 161 TRP 0.033 0.002 TRP B 117 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00334 (10566) covalent geometry : angle 0.70476 (14366) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.42475 ( 12) hydrogen bonds : bond 0.03654 ( 577) hydrogen bonds : angle 4.32794 ( 1731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.75 seconds wall clock time: 35 minutes 48.19 seconds (2148.19 seconds total)